China is one of the regions with the most frequent drought disasters and serious social and economic losses. Agricultural drought loss is one the most serious natural disasters. Due to climate change, the regional agricultural drought risk assessment has always been the focus of the academic circle. This study takes Zunyi City as an example, which is the most typical City of karst landform development. The monthly precipitation data set of ground meteorological observation stations in Zunyi City from 1956 to 2020 was selected, and the drought characteristic variables were extracted by the coupled use of the precipitation anomaly percentage (Pa) index and the theory of runs. The Copula function was applied to establish the joint distribution model of characteristic variables, obtaining the drought frequency and drought return periods. Combined with the Jensen model, the agricultural drought loss rate under different drought return periods in the target year (2020) was calculated and evaluated. The results showed that the Gumbel-Hougaard copula function was suitable for the joint distribution of drought joint variables in Zunyi City. From 1956 to 2020, fewer droughts occurred in Zhengan and Wuchuan, and the most droughts took place in Fenggang, Meitan, and Yuqing. The average drought duration in each county was about 1.5 months, and the average drought severity was about 0.35 in spatial distribution. Crop loss rate caused by drought increased and the affected area expanded with the increase of drought return periods (5, 10, 20, 50, and 100 years) in temporal distribution. Meanwhile, the drought disaster was most drastic in the eastern region, followed by the south, north, west, and central area. The results were highly consistent with the historical drought in Zunyi City, which verified the validity of the model. This study could provide scientific knowledge for drought resistance and reasonable mitigation programing for the security of the regional agricultural production and the sustainability of social and economic development.