Due to the combinatorial nature of cell formation problem and the characteristics of multi-objective and multi-constrain, a novel method of evolutionary algorithm with preference is proposed. The analytic hierarchy process (AHP) is adopted to determine scientifically the weights of the sub-objective functions. The satisfaction of constraints is considered as a new objective, the ratio of the population which doesn’t satisfy all constraints is assigned as the weight of new objective. In addition, the self-adaptation of weights is applied in order to converge more easily towards the feasible domain. Therefore, both features multi-criteria and constrains are dealt with simultaneously. Finally, an example is selected from the literature to evaluate the performance of the proposed approach. The results validate the effectiveness of the proposed method in designing the manufacturing cells.