Due to the limited distance of beacon operating, stumbling block, etc. in long BaseLine (LBL) acoustic positioning system, the Unmanned Underwater Vehicle (UUV) may not receive the entire response signals, and cause the measurement update delay. The paper focuses the navigation filter algorithm for the above conditions. Combined the error model of Strapdown Inertial Navigation System (SINS) and the error of sound velocity, the SINS/LBL integrated navigation model is built. An asynchronous measurement sequential processing method is introduced into the SINS/LBL integrated navigation algorithm to optimize the filtering process and achieve measurement update in time. The positioning error between the sequential filter algorithm and the conventional algorithm in SINS/LBL integrated navigation is compared via lake trial data analysis. The results show that this method can perform measurement update timely using limited observed values of responding signal and guarantee the navigation precision, even when some responding signal is missing.