Focusing on the cultivated land in Wanjiang Economic Zone, 338 sets of soil samples of rice, wheat, and their roots were collected; the concentrations of five heavy metals (As, Cd, Cr, Hg, and Pb) were determined; the soil-crop pollution characteristics were evaluated using the method of geo-accumulation index and comprehensive evaluation; the human health risk of ingesting heavy metals from crops was assessed; and the soil environmental reference value of the regional cultivated land was inverted based on the species sensitive distribution model (SSD). The results showed that in the study area, the soil of rice and wheat was polluted by heavy metals (As, Cd, Cr, Hg, and Pb) in varying degrees, among which Cd was the primary pollution factor of rice, with the over-standard rate of 13.33%, and Cr was the main over-standard factor of wheat, with the over-standard rate of 11.32%. The cumulative index showed that the percentage of Cd pollution in rice was 80.7%, and that in wheat was 35.85%. Contrary to the high pollution level of soil heavy metals, only 17.19% and 7.55% of Cd in rice and wheat exceeded the national food safety limit, and the accumulation capacity of the heavy metal Cd was rice>wheat. The health risk assessment indicated that heavy metals had high non-carcinogenic risk and unacceptable carcinogenic risk to adults and children in this study. The carcinogenic risk of rice intake was higher than that of wheat, and the health risk of children was higher than that of adults. SSD inversion showed that the reference values of As, Cd, Cr, Hg, and Pb in paddy soil in the study area were an HC5 of 6.24, 0.13, 258.27, 0.12, and 53.61 mg·kg-1 and an HC95 of 68.81, 5.71, 1068.92, 0.80, and 174.22 mg·kg-1, respectively. The reference values of As, Cd, Cr, Hg, and Pb in wheat soil HC5 were 32.99, 0.04, 271.14, 0.09, and 47.53 mg·kg-1, and the values of HC95 were 225.28, 0.71, 998.58, 1.43, and 241.99 mg·kg-1, respectively. The reverse analysis showed that the HC5 of heavy metals in rice and wheat were lower than the soil risk screening values in the current standard to varying degrees. The current soil standard had loosened for the evaluation results of this region.