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Separation operation in the experiment of DNA computing can separate DNA strands according to only one bit. It always need repeat the separation operation many times when solving actual problems; so it is very inefficient and time-exhausted. In order to solve this problem, Multi-separation techniques were proposed, and a multi-separation equipment model was designed, too. A DNA algorithm of The graph vertex coloring (GVC) Problem was proposed by using the idea of converting the problem into a satisfy-ability (SAT) problem. The multi-separation techniques were implied to solve GVC problem. The experiment steps were given through an instance; and the final correct coloring schemes were obtained, too. Comparing to other DNA algorithms of GVC problem, the multi-separation-based algorithm need less experiment steps and less DNA codes. At last, both the feasibility of the algorithm and the validity of multi-separation techniques were proved by the instance.