Abstract: Naoli River Basin is located within the Sanjiang Plain in Heilongjiang Province, China. The agricultural structure of Sanjiang Plain has been greatly adjusted with a large amount of dry land crops into wetland rice since the early 2000s, thereby resulting in a series of problems in the utilization of water resources in Naoli River Basin. Therefore, it is necessary to explore the water profit and loss situation of main crops, in order to implement regional irrigation strategies, and thereby to serve as the national food security. In this study, the Priestley Taylor formula, and Crop Water Surplus and Deficit Index (CWSDI) were used to reveal the water profit and loss situation of the middle rice, spring wheat and spring maize, in Naoli River Basin. The fundamental resources included the MODIS image, the long-term sequenced meteorological and the DEM data sets during the processing. Results showed that the Potential Evapotranspiration (ET0) increased from 910.25 mm in 2000 to 964.04 mm in 2015 in this river basin. The water demand of main crops, including middle crop, spring wheat and spring maize, also increased at different ranges as a whole. There was a decrease trend in the CWSDI from 2000 to 2015 in Naoli River Basin, indicating the natural precipitations can not meet the irrigation demand of middle rice, while the absolute value of index increased from the northeast to southwest in the spatial distribution. The CWSDI of spring wheat was larger than that of the middle rice, showing similar characteristics in the whole spatial distribution for each year. The CWSDI of spring maize indicated that the spatial characteristics of northwest were slightly lower than that of the southeast, indicating both regions in the condition of mild water shortage in Naoli River Basin. Drought classification was also evaluated using the CWSDI. The middle rice, accounting for the area proportion of 143.46%, was basically in mild drought state in the research basin. Despite at the state of water shortage, spring wheat has not reached the drought standard. The cultivated area of spring maize has decreased by 79.90% in the mild drought state in Naoli River Basin. The reason can be that the spring wheat and spring maize have been partly substituted for the middle rice with a rapid increasing trend since 2000, and thereby the planting of wetland crops, such as rice, led to a severe shortage of water. The spring wheat and spring maize demonstrated an extremely rare negative impact on the water surplus and deficit situation. These findings can provide the promising references when implementing the farmland irrigation schemes and agricultural structure adjustment in Naoli River Basin, China.