Crop production in the Northeast Farming Region of China (NFR) is affected considerably by variation in climatic conditions. Data on crop yield and weather conditions from a number of agro-meteorological stations in NFR were used in a mixed linear model to evaluate the impacts of climatic variables on the yield of maize (Zea mays L.), rice (Oryza sativa L.), soybean (Glycine max L. Merr.) and spring wheat (Triticum aestivum L.) in different crop growth phases. The crop growing season was divided into three growth phases based on the average crop phenological dates from records covering 1981 and 2010 at each station, comprising pre-flowering (from sowing to just prior to flowering), flowering (20 days around flowering) and post-flowering (10 days after flowering to maturity). The climatic variables were mean minimum temperature, thermal time (which is used to indicate changes in the length of growth cycles), average daily solar radiation, accumulated precipitation, aridity index (which is used to assess drought stress) and heat degree-days index (HDD) (which is used to indicate heat stress) were calculated for each growth phase and year. Over the 1961–2010 period, the minimum temperature increased significantly in each crop growth phase, the thermal time increased significantly in the pre-flowering phase of each crop and in the post-flowering phases of maize, rice and soybean, and HDD increased significantly in the pre-flowering phase of soybean and wheat. Average solar radiation decreased significantly in the pre-flowering phase of all four crops and in the flowering phase of soybean and wheat. Precipitation increased during the pre-flowering phase leading to less aridity, whereas reduced precipitation in the flowering and post-flowering phases enhanced aridity. Statistical analyses indicated that higher minimum temperature was beneficial for maize, rice and soybean yields, whereas increased temperature reduced wheat yield. Higher solar radiation in the pre-flowering phase was beneficial for maize yield, in the post-flowering phase for wheat yield, whereas higher solar radiation in the flowering phase reduced rice yield. Increased aridity in the pre-flowering and flowering phases severely reduced maize yield, higher aridity in the flowering and post-flowering phases reduced rice yield, and aridity in all growth phases reduced soybean and wheat yields. Higher HDD in all growth phases reduced maize and soybean yield and HDD in the pre-flowering phase reduced rice yield. Such effects suggest that projected future climate change may have marked effects on crop yield through effects of several climatic variables, calling for adaptation measures such as breeding and changes in crop, soil and agricultural water management.