More than a million Japanese encephalitis (JE) cases occurred in mainland China from the 1960s to 1970s without vaccine interventions. The aim of this study is to analyze the spatial and temporal pattern of JE cases reported in mainland China from 1965 to 1973 in the absence of JE vaccination, and to discuss the impacts of climatic and geographical factors on JE during that period. Thus, the data of reported JE cases at provincial level and monthly precipitation and monthly mean temperature from 1963 to 1975 in mainland China were collected. Local Indicators of Spatial Association analysis was performed to identify spatial clusters at the province level. During that period, The epidemic peaked in 1966 and 1971 and the JE incidence reached up to 20.58/100000 and 20.92/100000, respectively. The endemic regions can be divided into three classes including high, medium, and low prevalence regions. Through spatial cluster analysis, JE epidemic hot spots were identified; most were located in the Yangtze River Plain which lies in the southeast of China. In addition, JE incidence was shown to vary among eight geomorphic units in China. Also, the JE incidence in the Loess Plateau and the North China Plain was showed to increase with the rise of temperature. Likewise, JE incidence in the Loess Plateau and the Yangtze River Plain was observed a same trend with the increase of rainfall. In conclusion, the JE cases clustered geographically during the epidemic period. Besides, the JE incidence was markedly higher on the plains than plateaus. These results may provide an insight into the epidemiological characteristics of JE in the absence of vaccine interventions and assist health authorities, both in China and potentially in Europe and Americas, in JE prevention and control strategies.