A method of controlling a power trunk or a power tailgate in a power trunk or tailgate control system for controlling operations of the power trunk or the power tailgate in a vehicle having the power trunk or the power tailgate, the method comprising: checking whether the power trunk or the power tailgate has an open operation state or a close operation state; measuring a Hall effect count of a left spindle motor for driving a left spindle and a Hall effect count of a right spindle motor for driving a right spindle used to open or close the power trunk or the power tailgate if the power trunk or the power tailgate has the open operation state or the close operation state; stopping operations of the left and right spindle motors and outputting an alarm if an error count is equal to or greater than a predetermined error limitation value as a result of the measurement of the Hall effect count of the left spindle motor and the Hall effect count of the right spindle motor; stopping operations of the left and right spindle motors, and outputting an alarm if a difference of the Hall effect counts obtained by comparing the Hall effect count of the left spindle motor and the Hall effect count of the right spindle motor is equal to or greater than a first predetermined limitation value; performing a synchronization procedure between the left and right spindles, if the difference of the Hall effect counts is smaller than the first limitation value and is equal to or greater than a second predetermined limitation value; and maintaining the current output ratio between the left and right spindle motors, if the difference of the Hall effect count is smaller than the second limitation value, characterized in that the Hall effect count of the right spindle motor is compared by referencing the Hall effect count of the left spindle motor, wherein performing the synchronization procedure includes increasing the output ratio of the right spindle motor if the power trunk or the power tailgate has the open operation state, and the Hall effect count of the right spindle motor is smaller than the Hall effect count of the left spindle motor, and decreasing the output ratio of the right spindle motor if the Hall effect count of the right spindle motor is greater than the Hall effect count of the left spindle motor. checking whether the power trunk or the power tailgate has an open operation state or a close operation state; measuring a Hall effect count of a left spindle motor for driving a left spindle and a Hall effect count of a right spindle motor for driving a right spindle used to open or close the power trunk or the power tailgate if the power trunk or the power tailgate has the open operation state or the close operation state; stopping operations of the left and right spindle motors and outputting an alarm if an error count is equal to or greater than a predetermined error limitation value as a result of the measurement of the Hall effect count of the left spindle motor and the Hall effect count of the right spindle motor; stopping operations of the left and right spindle motors, and outputting an alarm if a difference of the Hall effect counts obtained by comparing the Hall effect count of the left spindle motor and the Hall effect count of the right spindle motor is equal to or greater than a first predetermined limitation value; performing a synchronization procedure between the left and right spindles, if the difference of the Hall effect counts is smaller than the first limitation value and is equal to or greater than a second predetermined limitation value; and maintaining the current output ratio between the left and right spindle motors, if the difference of the Hall effect count is smaller than the second limitation value, characterized in that the Hall effect count of the right spindle motor is compared by referencing the Hall effect count of the left spindle motor, wherein performing the synchronization procedure includes increasing the output ratio of the right spindle motor if the power trunk or the power tailgate has the open operation state, and the Hall effect count of the right spindle motor is smaller than the Hall effect count of the left spindle motor, and decreasing the output ratio of the right spindle motor if the Hall effect count of the right spindle motor is greater than the Hall effect count of the left spindle motor.