In order to accurately differentiate and evaluate the efficiency of blue and green water use in paddy rice fields, the blue and green water differentiation model and water use efficiency evaluation index system were established based on the daily experimental observation of blue and green water interaction migration process during the whole crop season. Blue and green water use of paddy fields in Nanjing, China under different precipitation conditions were revealed. Results showed that annual field water inflow in 2015-2018 was measured to be 1, 322.9 mm (30.7% blue), 572.3, 246.0, and 375.2 mm of which were discharged in forms of surface drainage, evapotranspiration and leakage. Green (GE) and blue (BE) water efficiency in the whole growth period were calculated as 0.425 and 0.490, respectively, both of which were significantly higher in drought years than in wet years. Net blue (BP) and green (GP) water productivity were 4.334 and 2.301 kg/m3, respectively, and the latter was insignificantly affected by precipitation. BE and GP obtained by conventional method were 46.2% and 29.7% higher than those calculated by the proposed method. Field irrigation efficiency would be overestimated and the contribution of precipitation in crop production would be underrated if the interactive blue and green water migration process was ignored. The method and results of this study can provide a new approach for the evaluation of crop water footprint and agricultural blue and green water use efficiency.