Organic wastes have a positive impact on soil physical and chemical properties in the agroecosystems. However, its main effects on soil organic carbon (SOC) or total organic carbon, TOC (SOC and coal-C) contents as well as their effects on soil physico-chemical properties are still unclear. Two types of organic wastes (maize straw and manure) were utilized in dryland affected by mining activities to quantify their relative effect on soil physico-chemical properties. Regression analysis was used to assess the relationship between the soil physical properties, SOC, and TOC as well as their respective contributions to improving these properties. Treatments included control (CK), straw (S), low manure (LM), medium manure plus straw (S-MM), and high manure plus straw (S-HM). The results showed that SOC, soil bulk density, mean weight diameter (MWD), soil total porosity, soil penetration resistance, saturated hydraulic conductivity, and soil infiltration rate were strongly influenced by the application of organic wastes. A stronger linear relationship between SOC and the MWD, (R2 = 0.93, p < 0.05) compared to that between TOC and MWD indicated the important role of SOC in improving soil aggregation relative to the effect of TOC. According to the principal component analysis (PCA), the application of organic wastes had stronger effects on SOC contents and physical properties than TOC (SOC and coal-C). These findings advance our understanding of the actual effect of organic wastes on soil physical properties and SOC in dryland affected by mining activities and could inform fertilizer management decisions to improve soil properties.