The interrupted-sampling repeater jamming (ISRJ) is coherent and has the characteristic of suppression and deception to degrade the synthetic aperture radar (SAR) image quality. The anti-ISRJ methods are studied in this work in order to suppress the ISRJ based on the waveform and filter design for SAR. First, the relationship between the ISRJ and waveform is obtained by analyzing the principle of the ISRJ using the ambiguity function. The ISRJ produces multiple false targets based on the high Doppler tolerance of waveform and the characteristic of the matched filter. Next, a method is proposed to counter the ISRJ by transmitting a phase-coded (PC) waveform with low Doppler tolerance and designing the corresponding mismatched filter. The joint design method is then developed to improve the anti-ISRJ and imaging performance. In the proposed methods, the majorization minimization framework is introduced to solve the nonconvex waveform and filter design problem. Finally, several simulations are conducted to demonstrate the effectiveness of the proposed methods. Simulation results show that the joint design method shows better anti-ISRJ and imaging performance in comparison with the separate design method, but it is more sensitive to the ISRJ sampling duty ratio and period.