The microlens array has been widely applied in LED lighting source due to its special optical properties, but most of the research lacks the analysis and optimization of the complete mathematical models. Hence, the new design method of a free-form surface microlens array optical system is proposed in this paper. Based on the characteristics of TIR and the law of refraction, a complete mathematical model of the free-form microlens is established. By numerically solving a set of differential equations, the profile of the free-form surface microlens is obtained. Then we rotate the profile to get the free-form surface microlens. Finally, the proposed microlens array is simulated and analyzed in near-field and far-field situations, respectively. We also discuss the influence of microlens array characteristics on illumination performance. The result shows the uniformity and efficiency have been improved, both of which can reach more than 90%.