In this paper we present the study of the transversal and longitudinal acceptance and the transmission efficiency in the injection, acceleration, and extraction systems in the separated sector cyclotron of the heavy ion research facility in Lanzhou, China. The study of cyclotron acceptance is done for 238U36+ with energy of 97 MeV/u and for 70Zn10+ with energy of 5.62 MeV/u under the theoretical isochronous and real magnetic field distribution. From the simulation results it can be seen that the transmission efficiency and the acceptances of separated sector cyclotron can be improved by redesign the curvature of MSI3 deflector or by introducing the magnet shim in MSI3 deflector region to change the distribution of the inner magnetic field.