Urban runoff is a major cause of urban flooding and is difficult to monitor in the long term. In contrast, long term continuous rainfall data are generally available for any given region. As a result, it has become customary to use design rainfall depth as a proxy for runoff in urban hydrological analyses, with an assumption of the same frequency for runoff and rainfall. However, this approach has lack of overall coordination and cannot fully reflect the variability of rainfall characteristics. To address this issue, this study presents a three-dimensional copula-based multivariate frequency analysis of rainfall characteristics based on a long term (1961–2012) rainfall data from Guangzhou, China. Firstly, continuous rainfall data were divided into individual rainfall events using the rainfall intensity method. Then the characteristic variables of rainfall (design rainfall depth, DRD; total rainfall depth, TRD; peak rainfall depth, PRD) were sampled using the annual maximum method. Finally, a copula method was used to develop the multivariate joint probability distribution and the conditional probability distribution of rainfall characteristics. The results showed that the copula-based method is easy to implement and can better reflect urban rainstorm characteristics. It can serve a scientific reference for urban flood control and drainage planning.