Soil erosion decreases topsoil depth on hill slopes and increases depth in depositional areas, and hence impacts soil fertility and crop productivity in agricultural systems. However, it is not clearly elucidated how different crop species adapt to soil erosion regarding root function, nutrient uptake, and rhizosphere biochemical properties, which is pivotal to cropping strategy. We established three simulated erosion severities with topsoil depths of 10, 20, and 30 cm on a Mollisol farmland under a maize-soybean rotation system with no-tillage (zero-tillage). After three consecutive years of field experiment, the decrease in topsoil thickness from 30 to 10 cm resulted in 9-22% decrease in maize yield but no impact on soybean yield. Compared to the 30- and 20-cm topsoil thickness, the 10-cm topsoil significantly lowered root and shoot biomass of maize at the jointing (V7) and milk stages (R3) and of soybean at the mid-seed filling stage (R6). Compared to the 30-cm topsoil treatment, the 10-cm topsoil decreased available N and P in soil by 42 and 36% under maize, and by 25 and 19% under soybean, respectively, while the shallow topsoil also decreased ratios of N, P, and K content to root length with the decreases being less for maize than soybean. Compared to the 30-cm topsoil depth, the 10- and 20-cm topsoil significantly increased the activities of urease, phosphatase, and invertase in maize rhizosphere soil, but not in soybean rhizosphere soil except for the activity of urease in 10-cm topsoil. These results indicated that maize was more sensitive to thinning of topsoil than soybean due to the reduced soil nutrient availability and its capability to extract nutrients from the soil. The greater stimulation of nutrient mineralization processes in soil did not alleviate the nutrient constraint to maize yield under shallow topsoil conditions. Thus, it is increasingly important to develop fertilization strategy to maintain nutrient supply for maize rather than soybean when these crops are grown in the shallow topsoil.