To make high-speed counter-current chromatograph’s planetary transmission mechanism run stably, through the analysis of traditional prefabricated balance hole design algorithm and the verification of simulation software Matlab, a modified prefabricated balance hole design algorithm was proposed. The modified prefabricated balance hole design algorithm was applied in the balance hole design of chromatograph planetary mechanism separation column. Combined with residual unbalance of separation column, the balance hole structure of rotor was modeled. Dynamic balance tests were conducted to compare balance effects of planetary mechanism using two balance hole layouts. The dynamic balance test data showed that the unbalance reduction rate of separation column with modified balance hole structure is 9.9% higher than that of separation column with traditional balance hole structure, the unbalance reduction rate of planetary mechanism with modified balance hole structure is 18.2% higher than that of planetary mechanism with traditional balance hole structure; the balance accuracy of planetary mechanism with modified balance hole structure is significantly improved compared with that of planetary mechanism with traditional balance hole structure.