Secure precision time synchronization is important for applications of Cyber-Physical Systems. However, several attacks, especially the Time Delay Attack (TDA), deteriorates the performance of time synchronization system seriously. Multiple paths scheme is thought as an effective security countermeasure to decrease the influence of TDA. However, the effective secure combination algorithm is still missed for precision time synchronization. In this paper, a secure combination algorithm based on Dempster-Shafer theory is proposed for multiple paths method. Special optimizations are done for the combination algorithm to solve the potential problems due to untrusted evidence. Theoretical simulation shows that the proposed algorithm works much better than Fault Tolerant Algorithm (FTA) and the attack detection method based on single path. And experimental demonstration proves the feasibility and superiority of the proposed algorithm, where the time stability with 27.97 ps, 1.57 ps, and 1.12 ps at average time 1s, 10s, 100s is achieved under TDA and local clock jump. The proposed algorithm can be used to improve the security and resilience of many importance synchronization protocol, such as NTP, PTP, and TWFTT.