Rapid and accurate mapping of soil properties in farmlands is crucial for guiding agricultural production and maintaining food security. Traditional methods using spectral features from remote sensing prove valuable for estimating soil properties, but are restricted to short periods of bare soil occurrence within agricultural settings. Addressing the challenge of predicting soil properties under crop cover, this study proposed an improved soil modeling framework that integrates dynamic crop growth information with machine learning techniques. The methodology’s robustness was tested on six key soil properties in an agricultural region of China, including soil organic carbon (SOC), total nitrogen (TN), total phosphorus (TP), dissolved organic carbon (DOC), dissolved organic nitrogen (DON), and pH. Four experimental scenarios were established to assess the impact of crop growth information, represented by the normalized difference vegetation index (NDVI) and phenological parameters. Specifically, Scenario I utilized only natural factors (terrain and climate data); Scenario II added phenological parameters based on Scenario I; Scenario III incorporated time-series NDVI based on Scenario I; and Scenario IV combined all variables (traditional natural factors and crop growth information). These were evaluated using three advanced machine learning models: random forest (RF), Cubist, and Extreme Gradient Boosting (XGBoost). Results demonstrated that incorporating phenological parameters and time-series NDVI significantly improved model accuracy, enhancing predictions by up to 36% over models using only natural factors. Moreover, although both are crop growth factors, the contribution of the time-series NDVI variable to model accuracy surpassed that of the phenological variable for most soil properties. Relative importance analysis suggested that the crop growth information, derived from time-series NDVI and phenology data, collectively explained 14–45% of the spatial variation in soil properties. This study highlights the significant benefits of integrating remote sensing-based crop growth factors into soil property inversion under crop-covered conditions, providing valuable insights for digital soil mapping.