The array structure is widely used in precise electronic products such as large phased array antennas and large optical telescopes, the main components of which are a large surface base and a large number of high-precision discrete elements mounted on the surface base. The geometric error of discrete elements is inevitable in the manufacturing process and will seriously degrade the product performance. To deal with the tolerance design of discrete elements, a region-division-based tolerance design method is proposed in this paper. The whole array was divided into several regions by our method and the tolerance of discrete elements was correlated with the region importance on the performance. The method specifically includes the following steps: first, the sensitivity of the product performance to geometric errors was analyzed and the statistical relationship between the performance and geometric errors was established. Then, based on the sensitivity matrix, the regional division scheme was developed, and the corresponding tolerance was optimized according to the established relationship function. Finally, the optimal tolerance was selected among the multiple solutions to achieve the best performance. Taking a large phased array as an example, a simulation experiment was performed to verify the effectiveness of the proposed method.