Soil parameters, measured before crop planting, are typically used to quantify the relationship between soil properties and crop yield and to identify factors limiting crop yield. However, soil properties during sensitive stages of crop growth may have a greater effect on crop yield than the initial values. We determined if inclusion of soil properties, measured during the reproductive stage, could improve the accuracy of crop yield prediction. Classification and regression trees were used to determine the explanatory power of different soil and rice variables for predicting rice yield in alkaline salt-affected paddy fields in northeast China. The traditional method explained 77.5% of the rice yield variation and identified soil CO32- in the 0- to 10-cm soil layer, with single explanatory power of 53.4%, as the most important predictor. The whole explanatory power of the methods including soil variables during the reproductive stage and yield components, with/without soil variables before planting, increased to 81.3%. The residual sodium carbonate, measured in the 0- to 10-cm soil layer during the reproductive stage, was identified as the most limiting factor due to its single maximum explanatory power of 60.5%. We conclude that inclusion of soil properties, measured during the reproductive stage, has potential for improving the rice yield prediction accuracy by enhancing the explanatory power in identification of the most limiting factor. These results encourage further investigation of the role of soil properties during sensitive stages of crop growth in crop yield prediction under different soil and climatic conditions.