A medical image processing system comprising: a medical image acquisition unit that acquires a medical image obtained by imaging an observation target; a feature amount calculation unit that calculates a feature amount of the observation target for each of pixels of an image region of the medical image or for each of divided regions obtained by dividing the image region of the medical image into a specific size; and a stage determination unit that determines a disease stage of the observation target by using a spatial distribution of the feature amount, wherein the stage determination unit determines between an early stage and a progress stage, and a variation in the spatial distribution of the feature amount in the progress stage is larger than a variation in the spatial distribution of the feature amount in the early stage; wherein the stage determination unit includes: a distribution index value calculation unit that calculates a distribution index value which is an index value of the spatial distribution of the feature amount; a determination unit that determines the disease stage based on the distribution index value; and a first region integration unit that integrates abnormal regions indicating a pixel or a divided region where the feature amount is outside a specific range, in case where the abnormal regions are distributed adjacent to each other, among integrated abnormal regions (IR1, IR2, IR3) in which the abnormal regions are integrated by the first region integration unit, the integrated abnormal region whose area is equal to or larger than a certain value is set as a specific integrated abnormal region, and the integrated abnormal region (IR1, IR2) whose area is less than the certain value is not set as the specific integrated abnormal region, and the distribution index value is an index value related to a spatial distribution of the specific integrated abnormal region. a medical image acquisition unit that acquires a medical image obtained by imaging an observation target; a feature amount calculation unit that calculates a feature amount of the observation target for each of pixels of an image region of the medical image or for each of divided regions obtained by dividing the image region of the medical image into a specific size; and a stage determination unit that determines a disease stage of the observation target by using a spatial distribution of the feature amount, wherein the stage determination unit determines between an early stage and a progress stage, and a variation in the spatial distribution of the feature amount in the progress stage is larger than a variation in the spatial distribution of the feature amount in the early stage; wherein the stage determination unit includes: a distribution index value calculation unit that calculates a distribution index value which is an index value of the spatial distribution of the feature amount; a determination unit that determines the disease stage based on the distribution index value; and a first region integration unit that integrates abnormal regions indicating a pixel or a divided region where the feature amount is outside a specific range, in case where the abnormal regions are distributed adjacent to each other, among integrated abnormal regions (IR1, IR2, IR3) in which the abnormal regions are integrated by the first region integration unit, the integrated abnormal region whose area is equal to or larger than a certain value is set as a specific integrated abnormal region, and the integrated abnormal region (IR1, IR2) whose area is less than the certain value is not set as the specific integrated abnormal region, and the distribution index value is an index value related to a spatial distribution of the specific integrated abnormal region. a distribution index value calculation unit that calculates a distribution index value which is an index value of the spatial distribution of the feature amount; a determination unit that determines the disease stage based on the distribution index value; and a first region integration unit that integrates abnormal regions indicating a pixel or a divided region where the feature amount is outside a specific range, in case where the abnormal regions are distributed adjacent to each other, among integrated abnormal regions (IR1, IR2, IR3) in which the abnormal regions are integrated by the first region integration unit, the integrated abnormal region whose area is equal to or larger than a certain value is set as a specific integrated abnormal region, and the integrated abnormal region (IR1, IR2) whose area is less than the certain value is not set as the specific integrated abnormal region, and the distribution index value is an index value related to a spatial distribution of the specific integrated abnormal region.