Based on the high-precision and high-quality data of eight heavy metals obtained from the 1∶250,000 multi-purpose regional geochemical survey in Fujian Province, this study investigated the topsoils (depths: 0~20 cm) throughout the province, with reference to the Environmental Quality Standard for Soils (GB 15618—2018). A geochemical assessment method for soil environmental quality based on individual/composite indices, matching the structural characteristics of the assessment standard, was developed to first assess the environmental quality of topsoils across Fujian Province. The results indicate that the topsoils in Fujian Province are dominated by strongly acidic and acidic soils, representing 36.5% and 57.89% of the total area in the province, respectively. The soils for prioritized conservation cover 91.06% of the total area, suggesting overall high soil environmental quality in the province. The over-limit ratio of 8.94% for soil heavy metals in the province is significantly below the total over-limit ratio of 16.1% in China. The element with the highest over-limit ratio is Pb, accounting for 4.95%, followed by Cd, accounting for 2.84%. In contrast, elements like Zn, Hg, Cu, As, Ni, and Cr show minimal over-limit ratios. Regarding the spatial distribution characteristics of topsoil elements, zones with over-limit Pb, Cd, Zn, Cu, As, and Cr are primarily distributed in the metal or non-metal sulfide deposits/ore occurrences/mineralized spots within the Wuyishan metallogenic belt and their surrounding areas. Zones with over-limit Hg are primarily distributed in the junction zone between Youxi and Dehua counties, as well as in cities along the coastal area of Fujian Province. The zone with over-limit Ni is predominantly located in the geological background area of the Fotan Formation basalts and olivine basalts in the northeast of Zhangpu County. Overall, the soil environmental quality is higher in the coastal area compared to the inland area. The assessment results of this study fill the gap in the geochemical assessment of soil environmental quality in Fujian Province, first providing the comprehensive geochemical assessment data of soil environmental quality for the province. These data, revealing the environmental quality of soil resources in Fujian Province, serve as fundamental geochemical data for scientific research in related fields and for constructing the geological information engineering big data platform for Fujian Province. Overall, this study provides a decision-making reference for soil environment management, territorial space planning, and the construction of the national ecological civilization pilot zone (Fujian) in Fujian Province, holding significant scientific value.