Respiratory infectious diseases (RID) are the major form of infectious diseases in China, and are highly susceptible to climatic conditions. Current research mainly focuses on the impact of weather on RID, but there is a lack of research on the effect of El Niño–Southern Oscillation (ENSO) on RID. Therefore, this paper uses the system generalized method of moments (SYS-GMM) and the data of 31 provinces in China from 2007 to 2018 to construct a dynamic panel model to empirically test the causality between ENSO and RID morbidity. Moreover, this paper considers the moderating effects of per capita disposable income and average years of education on this causality. The results show that ENSO can positively and significantly impact RID morbidity, which is 5.842% higher during El Niño years than normal years. In addition, per capita disposable income and average years of education can effectively weaken the relationship between ENSO and RID morbidity. Thus, this paper is of great significance for improving the RID early climate warning system in China and effectively controlling the spread of RID.