The old algorithm to solve 0-1 planning problem using DNA computing only searches the feasible solution set from all solution set, then we give an algorithm which can search optimization solution of 0-1 planning problem from all solution set by encoding specially solution set, using technique of electrophoresis and fluorescence labeling technique, and then we give an example to explain the algorithm validity and correctness. We also give a kind of strategy to deal with the negative real number of value coefficient and the complexity of our algorithm is ( ) O m .