In the paper, to solve the problem of anti-jamming delay compensation of multi-system satellite navigation receiver, an adaptive compensation algorithm of anti-jamming delay is proposed, which can make the sampling time of different of different frequency points at the same time, and improve the precision of pseudo-range measurement and carrier measurement in anti-jamming state. The influence of different anti-jamming delay on the accuracy of observation is quantitatively analyzed and tested on a certain anti-jamming receiver. The test results show that the adaptive compensation algorithm designed in this paper is effective in adjusting the anti-jamming delay, eliminating the observation deviation introduced by the anti-jamming delay, and improving the positioning accuracy of the pseudo- range and carrier difference.