In hydraulic synchronous control system, the pressure jump generated by asymmetric cylinder during changing the direction results in the oscillation and even instability of the synchronous control system. Aiming at this problem, a method for eliminating pressure jump based on the dual-spool independent metering valve controlling asymmetric cylinder system was proposed. Firstly, the mechanisms of pressure jump generated by asymmetric cylinder were analyzed, in which the asymmetric cylinder was respectively controlled by traditional valve, asymmetric valve and dual-spool independent metering valve. Secondly, the models of traditional valve controlling asymmetric cylinder system and the dual-spool independent metering valve controlling asymmetric cylinder system were built in AMESim. Then the position following and the pressure jump in the traditional valve controlling asymmetric cylinder system and dual-spool independent metering valve controlling asymmetric cylinder system were compared and analyzed under different system pressures and different given signals. Finally, the experimental platform of the dual-spool independent metering valve controlling asymmetric cylinder system was built to verify the effectiveness of the proposed method. Simulation and experimental results showed that the asymmetric cylinder system controlled by the dual-spool independent metering valve can realize position following well through the fuzzy adaptive control algorithm. When the asymmetric cylinder changed direction, the pressure jump can be completely eliminated, reducing oscillation of the system, and made the system more stable. When the hydraulic cylinder was operated by square wave, the pressure impact was larger than that when the sine wave was operated. This method was beneficial to achieve good synchronous control effect.