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Purpose: With the development of mining and smelting activities, increasing concentrations of heavy metals are being taken into agricultural soil. The accumulation of heavy metals in soils and rice threatens humans. The objective of this study was to determine the source and the risk of heavy metals near a Pb-Zn mine and find out the main factor affecting heavy metal bioaccumulation in rice. Materials and methods: A total of 30 pairs of rice and surface soil samples were collected. The contents of Cd, Pb, As, Zn, Hg, Cu, and Ni in soil and rice grains were determined. The positive matrix factorization model was used to identify the source of heavy metals. The target hazard quotient and hazard index were calculated to evaluate human non-carcinogenic risk. Correlation analysis was used to find out the main factor affecting heavy metal bioaccumulation in rice. Results and discussion: The main pollutants were Pb, Cd, and Zn in soil and Pb and Cd in rice grains. The mining and smelting activities were the main reason for the high contents of Zn and Pb. The Cd was mainly attributed to the agricultural activities and high background value. The average values of the target hazard quotient of As and Cd in soil were both higher than 1. The local inhabitants were facing considerable non-cancer health risk from As and Cd. Moreover, soil pH and soil organic matter (SOM) played critical roles in the accumulation of heavy metals in rice grains. Conclusion: Mining activities have adverse effect on the surrounding soil and rice, increasing health risk for local residents. The measures of mining management, safe fertilizer-agrochemical utilization, and soil property improvement should be enforced in the mining area. The results of this study will provide a method basis for rice safety production in Guangxi. [ABSTRACT FROM AUTHOR]