An optical tracking system for tracking a patient and a surgical instrument for surgically treating the patient by using a three-dimensional image acquired in advance before surgical treatment for the patient, the optical tracking system comprising: a reference marker unit that is configured to be fixedly attached to a stationary object and not directly attached to the patient; a shape measurement unit configured to measure a three-dimensional shape of a specified part of the patient corresponding to the three-dimensional image; the surgical instrument including a marker and configured to surgically treat the patient; a tracking sensor unit configured to sense the reference marker unit, the shape measurement unit and the marker of the surgical instrument so as to track the reference marker unit, the shape measurement unit and the marker of the surgical instrument, respectively; and a processing unit configured to: acquire a first coordinate transformation relationship between the reference marker unit and the tracking sensor unit and a second coordinate transformation relationship between the shape measurement unit and the tracking sensor unit based on a sensing result of the tracking sensor unit; acquire a third coordinate transformation relationship between the specified part of the patient and the shape measurement unit based on a measurement result of the shape measurement unit; define a coordinate system of the patient relative to the reference marker unit from the first, second and third coordinate transformation relationships; acquire a fourth coordinate transformation relationship between the reference marker unit and the tracking sensor unit and a fifth coordinate transformation relationship between the marker of the surgical instrument and the tracking sensor unit based on a sensing result of the tracking sensor unit; and define a coordinate system of the surgical instrument relative to the patient using the fourth and fifth coordinate transformation relationships and the coordinate system of the patient relatively defined with respect to the reference marker unit. a reference marker unit that is configured to be fixedly attached to a stationary object and not directly attached to the patient; a shape measurement unit configured to measure a three-dimensional shape of a specified part of the patient corresponding to the three-dimensional image; the surgical instrument including a marker and configured to surgically treat the patient; a tracking sensor unit configured to sense the reference marker unit, the shape measurement unit and the marker of the surgical instrument so as to track the reference marker unit, the shape measurement unit and the marker of the surgical instrument, respectively; and a processing unit configured to: acquire a first coordinate transformation relationship between the reference marker unit and the tracking sensor unit and a second coordinate transformation relationship between the shape measurement unit and the tracking sensor unit based on a sensing result of the tracking sensor unit; acquire a third coordinate transformation relationship between the specified part of the patient and the shape measurement unit based on a measurement result of the shape measurement unit; define a coordinate system of the patient relative to the reference marker unit from the first, second and third coordinate transformation relationships; acquire a fourth coordinate transformation relationship between the reference marker unit and the tracking sensor unit and a fifth coordinate transformation relationship between the marker of the surgical instrument and the tracking sensor unit based on a sensing result of the tracking sensor unit; and define a coordinate system of the surgical instrument relative to the patient using the fourth and fifth coordinate transformation relationships and the coordinate system of the patient relatively defined with respect to the reference marker unit. acquire a first coordinate transformation relationship between the reference marker unit and the tracking sensor unit and a second coordinate transformation relationship between the shape measurement unit and the tracking sensor unit based on a sensing result of the tracking sensor unit; acquire a third coordinate transformation relationship between the specified part of the patient and the shape measurement unit based on a measurement result of the shape measurement unit; define a coordinate system of the patient relative to the reference marker unit from the first, second and third coordinate transformation relationships; acquire a fourth coordinate transformation relationship between the reference marker unit and the tracking sensor unit and a fifth coordinate transformation relationship between the marker of the surgical instrument and the tracking sensor unit based on a sensing result of the tracking sensor unit; and define a coordinate system of the surgical instrument relative to the patient using the fourth and fifth coordinate transformation relationships and the coordinate system of the patient relatively defined with respect to the reference marker unit.