A dynamic coupling time varying failure rate analysis method of a on-orbit space flexible gear mechanism comprises the seven steps that firstly, according to the fact that a shaft in the on-orbit space flexible gear mechanism is an elastic body, a kinetic equation of the flexible shaft is built, and the finite element method is adopted for analysis; secondly, a gear kinetic equation is built; thirdly, a nonlinear kinetics equation of coupling of the flexible shaft and a gear in the on-orbit space flexible gear mechanism is built; fourthly, transmission stimulation analysis is performed on the space flexible gear mechanism; fifthly, the Newmark algorithm is adopted to calculate a dynamic load coefficient; sixthly, a gear bending stress reliability limit state function is built in the on-orbit space flexible gear mechanism; seventhly, dynamic reliability and failure rate analysis are performed on the space flexible gear mechanism. The method solves the problem that reliability calculating accuracy is low because of nonlinear factors of a traditional transfer matrix method and mode superposition method, and has engineering practical value for improving reliability of the on-orbit space flexible gear mechanism and other spacecrafts. The method is also suitable for other flexible gear mechanisms.