The triple-frequency linear combination method can provide combinations with different characteristics and is one of the important methods to improve the performance of navigation services. Due to the large number of combinations and different combination performances, combinatorial clustering optimization is very important, and the efficiency of manual screening is very low. Firstly, based on the basic model, the objective equations are derived. Secondly, based on the fuzzy c-means (FCM) algorithm, three improved PSO-FCM algorithms are proposed, namely the S-PSO-FCM algorithm, L-PSO-FCM algorithm, and LOG-PSO-FCM algorithm. Thirdly, according to the different combination characteristics, the two datasets whose combined coefficients sum to 0 and 1 are emphatically discussed. Finally, the effectiveness of the improved PSO-FCM algorithms is studied based on the public dataset and the measured BeiDou-3 navigation satellite system (BDS-3) data of short baseline, long baseline, and ultra-long baseline. The results show that the performance of the proposed algorithm is better than that of the FCM algorithm, especially in short baseline and long baseline cases.