The injection, acceleration and extraction of sector-separated cyclotron(SSC) are analyzed and simulated to get the transverse and longitudinal acceptance, using two typical ions 238U36+ and 70Zn10+ with the energy of 9.7 MeV/u and 5.62 MeV/u respectively. In order to study the actual acceptance of SSC, the isochronous magnetic field model in coincidence with the real field is established by Kr-Kb and Lagrange methods on the basis of the actual measurement. The transverse and longitudinal acceptance is calculated under the above isochronous magnetic field model, and the main reason for the low efficiency and acceptance of SSC is the defaults in the design of MSI3 in the injection system and MSE3 in the extraction system. The results show that the