Sihui city (South China) is much affected by nasopharyngeal carcinoma (NPC). To investigate the relationships between the toxic metals in soil and NPC incidence in Sihui, 119 surface soil samples were collected from agricultural fields and analyzed. The soil As–Cr contents in Longjiang (high-incidence area) are significantly lower than those in Weizheng and Jianglin (low-incidence areas), whereas the soil Pb content in Longjiang is significantly higher than that in Weizheng. The Nemerow pollution indices (PIN) of soils decrease in the order of Jianglin > Weizheng > Longjiang. The enrichment factor (EF) of Cd indicates that the Cd enrichment is contributed by human activities. Potential toxic metal-related ecological risk values decrease in the order of Jianglin > Weizheng > Longjiang. The mean hazard index (HI) value of Longjiang was lower than those of Weizheng and Jianglin. There are no adverse noncarcinogenic health effects of soil toxic metals to adults in the study areas. Carcinogenic risks of As and Cr via ingestion and dermal contact and total carcinogenic risk are within the warning range, from 10−6 to 10−4. Hence, we suggest that toxic metals in the soil may not be major geochemical carcinogenic factors of high NPC incidence in Sihui.