Low-alloy wear-resistant steel often requires the addition of trace alloy elements to enhance its performance while also considering the cost-effectiveness of production. In order to comparatively analyze the strengthening mechanisms of Mo and Cr elements and further explore economically feasible production processes, we designed two types of low-alloy wear-resistant steels, based on C-Mn series wear-resistant steels, with individually added Mo and Cr elements, comparing and investigating the roles of the alloying elements Mo and Cr in low-alloy wear-resistant steels. Utilizing JMatPro software to calculate Continuous Cooling Transformation (CCT) curves, conducting thermal simulation quenching experiments using a Gleeble-3800 thermal simulator, and employing equipment such as a metallographic microscope, transmission electron microscope, and tensile testing machine, this study comparatively investigated the influence of Mo and Cr on the microstructural transformation and mechanical properties of low-alloy wear-resistant steels under different cooling rates. The results indicate that the addition of the Mo element in low-alloy wear-resistant steel can effectively suppress the transformation of ferrite and pearlite, reduce the martensitic transformation temperature, and lower the critical cooling rate for complete martensitic transformation, thereby promoting martensitic transformation. Adding Cr elements can reduce the austenite transformation zone, decrease the rate of austenite formation, and promote the occurrence of low-temperature phase transformation. Additionally, Mo has a better effect on improving the toughness of low-temperature impact, and Cr has a more significant improvement in strength and hardness. The critical cooling rates of C-Mn-Mo steel and C-Mn-Cr steel for complete martensitic transition are 13 °C/s and 24 °C/s, respectively. With the increase in the cooling rate, the martensitic tissues of the two experimental steels gradually refined, and the characteristics of the slats gradually appeared. In comparison, the C-Mn-Mo steel displays a higher dislocation density, accompanied by dislocation entanglement phenomena, and contains a small amount of residual austenite, while granular ε-carbides are clearly precipitated in the C-Mn-Cr steel. The C-Mn-Mo steel achieves its best performance at a cooling rate of 25 °C/s, whereas the C-Mn-Cr steel only needs to increase the cooling rate to 35 °C/s to attain a similar comprehensive performance to the C-Mn-Mo steel.