Evaluating the vulnerability of urban transportation systems to flood disasters can provide scientific support for urban disaster prevention and mitigation. Current methods for assessing the flood vulnerability of urban roads often overlook the internal relationships within the complex spatial composition of road networks and surface structures. In this study, based on the theory of complex networks, a dual-layer network assessment model is established for evaluating the flood vulnerability of urban transportation systems by coupling basic geographic data with road network vector data. Unlike traditional methods, this model considers the complex relationship between road network structures and ground surfaces, uncovering a correlation between road network structure and road flood vulnerability. By utilizing this model, the flood vulnerability of road networks in Shenzhen, as well as the city’s spatial flood vulnerability, are quantitatively assessed. Based on the quantitative results, we create maps illustrating the distribution of road and spatial flood vulnerability in Shenzhen. The study results reflect that roads highly vulnerable to flooding are mainly located in the central urban area of the southwest, with the flood vulnerability spatially concentrated primarily in the northern and western regions. Using data from government reports, news stories, and other sources over the past five years, we compile recorded instances of urban waterlogging. The quantitative results of the model are consistent with the distribution trend in recorded waterlogging points, indicating that the model’s outcomes are authentic and reliable.