The invention discloses a method for distributing time slots in a carrier channel in an MF-TDMA (Multi-Frequency Time Division Multiple Address) satellite system. The method comprises the following steps: taking a time slot resource tree as a management model; introducing a priority positioning method and a binary coding conversion time slot cutting method; re-arraying the received application number of the time slots of each user terminal according to a sequence from big to small and marking a priority level; and dividing the number of the time slots of each user terminal into the sum of 2n time slot blocks according to a binary conversion method. During the distributing process, the prior distribution for a user with a large application number of the time slots is ensured; the operation delay is reduced; a big time slot space is firstly occupied by a big time slot block according to a priority distributing method based on a right-keeping principle; the rejection for the application caused by a time slot space firstly occupied by a small time slot block is avoided, so that the generation of time slot fragment is effectively eliminated; and the use rate of the resources is increased.