Dengue fever is a rapidly spreading mosquito-borne disease. Previous studies have shown that dengue vector mosquitoes are weather sensitive, and the effect of temperature on dengue transmission has been confirmed. However, associations between rainfall events and dengue incidence are not consistent, and few studies have addressed the roles of the magnitude and frequency of rainfall events in dengue transmission. Therefore, the purpose of this study was to differentiate the long-term and short-term effects of rainfall variation on dengue transmission and to investigate these effects within different socio-ecological contexts in southern Taiwan, which is a high-epidemic tropical region. A negative binomial multilevel model with Gaussian serial correlation was used in this study to investigate the intra- and inter-annual rainfall variability to determine the effects of rainfall on dengue occurrence in the pre-epidemic and epidemic seasons. Our significant results indicate that short-term rainfall and dengue occurrence show a non-linear relationship in which medium rainfall during the dengue season poses the most significant risk. We also found that rainfall effects are interactive to the percentage of old houses. Our results show strong synergistic interactions between low rain frequency and old house percentage, and between cumulative rainfall and old house percentage, contributing to dengue outbreaks. Our findings also differentiate the effects of short-term and long-term rainfall in old built-up environments on dengue occurrence. This implies that during rainy periods, old neighborhoods may require more attention from the public and private sectors to improve environmental quality and promote resident health.