Against the background of frequent urban waterlogging disasters caused by global climate change, the vulnerability of distribution systems has become increasingly prominent. To address the blindness and inefficiency of traditional protective equipment layout, this paper proposes a two-stage optimization method based on risk zoning, aiming to scientifically guide the layout of protective equipment represented by waterproof transformers. First, the method integrates six core indicators including rainfall, elevation, and slope, and uses the Analytic Hierarchy Process (AHP) to conduct refined waterlogging risk zoning of the distribution network, dividing nodes into three risk levels: high, medium, and low. Taking this risk assessment result as a key input, a mixed-integer programming model with the goal of maximizing comprehensive benefits is constructed. Finally, the model is verified through a 25-node numerical example. The results show that through strategic layout, the model protects most loads including high-risk nodes with limited costs, and makes a strategic abandonment of low-value nodes in line with the optimization goal. This study has important practical significance for improving investment efficiency and urban power grid resilience.