Waterlogging disasters cause huge loss of life and property damage every year. In this research, a Copula-based optimization method is proposed to solve the problems in bivariate design of urban stormwater and drainage systems resulting from ignorance of precipitation temporal dependence and discrepancy between different design codes. Optimized design combinations of stormwater and drainage systems conditioned on given Kendall bivariate return periods or return periods of either system can be obtained using the optimization method for the case study of Zhongshan and Zhuhai. Results show that the temporal dependencies between precipitation series with different durations should be carefully considered, which can be sufficiently described by Copula functions. Based on the optimized design combinations, it is found that the planned return periods of stormwater systems in Sponge City Plans are underestimated for both Zhongshan and Zhuhai, which restricts the full use of the drainage systems. According to the optimized results, the planned return periods of stormwater systems in Zhongshan (Zhuhai) should be adjusted to 8.04 a (6.76 a) for the downtown area and 6.52 a (5.59 a) for other areas, conditioned on the planned return periods for P24 h in Sponge City Plans. The proposed optimization method provides a useful approach for the bivariate design of stormwater and drainage systems. The results of this research can give stakeholders references in compiling engineering plans for urban waterlogging prevention and help better balance the conflicts between waterlogging safety and economic efficiency. © 2022 by the authors. Licensee MDPI, Basel, Switzerland.