The purpose of this study is to evaluate the bio-accumulation of different soil-crop systems (SCSs) for heavy metals (HMs) and the geo-accumulation of different agricultural growing regions. The ecological risk (ER) assessment was conducted to understand the impact of intensive agricultural production on the environment. To achieve this aim, four typical crops, wheat, corn, potatoes, and leeks grown in the Jiao River Basin (JRB), were selected as the research objects. The concentrations of eight HMs, including copper (Cu), lead (Pb), zinc (Zn), nickel (Ni), chromium (Cr), cadmium (Cd), arsenic (As), and mercury (Hg) in crop tissue and soil were detected. The statistical analysis, including the geo-accumulation index (Igeo), geostatistical analysis, correlation and cluster analysis were then used to evaluate soil contamination and determine the source types of HMs. The results show that the average concentrations of eight HMs in the soil follow the order: Zn > Cr > Ni > Pb > Cu > As > Cd > Hg and the calculated concentration coefficients (K) vary from 0.41–1.12, indicating relative scarcity in sources of HMs. All the Igeo values of HMs are less than 0 except the Igeo of Cr within potato-farmland is from 0 to 1, illustrating that the soil in JRB is uncontaminated. The correlation and cluster analysis reveal that Cu, Zn, and Cd have a strong relationship with each other and the relationship between Pb, Ni, and Cr is general. The content of eight HMs in different crops varies greatly and most of them are within the scope of National Food Safety Standards—Limit of Pollutants in food of China. The bioconcentration factors (BCF) indicate that wheat, corn, potato, and leek have strong bio-accumulation ability of Cu, Zn, and Cd. The ecological risk factor (Er) shows that JRB is in low risk of Cu, Pb, Zn, Ni, Cr, and As; however, the risk of Cr and Hg are mostly low, characterized by partially dotted moderate risk. The risk index (RI) is mainly moderate with partially low risk distributed in planar and high risk distributed in point.