The effects and regulatory actions of the polychlorinated biphenyls (PCBs) substituent characteristics on their relative retention times (RRTs) during gas chromatography were analyzed based on known experimental RRTs of 209 PCB congeners and biphenyl; the substituent characteristics used for this analysis included the total amount of substituents, the similarity between two phenyl rings in a single PCB congener, the substituents distribution in single phenyl ring, the main/second-order interactions effects at each position, and the combined effect of two phenyl rings. At last, the universality of regulation was validated on other experimental conditions. Among them, the full factorial experimental design included 10 factors correlated with each substituent position and two levels (0, 1) were initially applied to the domains of the substituent characteristics. The obtained results have revealed that increasing the total amount of substituents can increase the RRTs of PCBs linearly, but similarities between the two rings cannot control the RRTs effectively. Meanwhile, the more compact the substituent distributions on a single phenyl ring are, the bigger the RRTs of PCBs are. Based on a full factorial experimental design, the overall important trend for each position is as follows: para > meta > ortho and the main regulatory substituents for the second-order interaction effects are distributed in the same phenyl ring in the following sequence: N o > N m > N p . The congener with two perpendicular phenyl rings exhibits a milder combined effect on RRTs and smaller RRT relatively. The regulation has a good universality among different experimental conditions, revealing the dominant effect of substituent characteristics on RRTs of PCBs.