The rational allocation of tolerances is the key to reduce production costs and guarantee the performance. In this paper, in the premise of ensuring the performance, manufacturing cost minimization of assembly parts is set as objective function, and an adaptive genetic algorithm is proposed to optimize the design of tolerance allocation. The adaptive mechanism is introduced mainly for crossover operator and mutation operator to overcome the traditional adaptive genetic algorithm’s easy "premature" shortcomings according to individual fitness of population. And a penalty function is used to handle constraints of assembly dimension chain. Finally, using the algorithm to optimize assembly chain tolerances of a gear reducer shaft, the effectiveness of the adaptive genetic algorithm to optimize tolerance allocation has been verified.