Abstract: Magnetic compressor is a very important part for SASE FEL facility at Peking University (PKU SASE FEL), which is used to produce short electron bunches in order to satisfy fast lasing saturation of SASE in undulator. In this paper, the fundamental principle of magnetic compression is analyzed, which shows that the effect of bunch compression is closely related with the RF instability. By using the design parameters of magnetic chicane of PKU SASE FEL, the impact on the magnetic compression due to RF instability is given. The final bunch length will change due to RF instability. So, a gool for RF instability control is proposed according to the requirement of PKU FEL.