Radiometric correction is essential to unmanned aerial vehicle (UAV) precision agriculture applications, especially for crop multi-period analysis and quantitative inversion of phenotypic and physiological parameters. In this study, we investigated the performance of four radiometric correction methods: “Camera only” (A), “Camera and sun irradiance” (B) and “Camera, sun irradiance and sun angle” (C) methods provided by Pix4d Mapper and an irradiance sensor-based method (D) implemented with the R software. UAV campaigns were conducted at flight altitudes of 30 m, 60 m and 90 m under clear and cloudy skies at different times over an experimental field of winter wheat. The influences of illumination, flight altitude and flight time on reflectance and vegetation indexes derived from different radiometric calibration methods were analyzed. Moreover, we further assessed the impact of reflectance and vegetation index variations on the above-ground biomass (AGB) and leaf area index (LAI) estimations of winter wheat. Results showed that method D is a promising approach for radiometric calibration, which produced consistent reflectance with method A at noon (e.g., 10:44:41 AM March 17 and 11:39:37 AM April 7) and mid-afternoon (e.g., 15:30:02 PM May 1) and more reliable reflectance in the morning (e.g., 7:15:44 AM March 17). Methods B and C seriously underestimated the reflectance at 10:44:41 AM March 17 and 11:39:37 AM April 7. This was caused by the incorrect attitude angles of the irradiance sensor and further miscalculation of the solar irradiance by Pix4d Mapper. Interestingly, these errors were eliminated in the calculation of the ratio type of vegetation indexes. Methods B and C yielded vegetation indexes that were almost the same as those of methods A and D. Under cloudy sky, when direct sunlight is not blocked by clouds, method D was effective; with cloud occlusion, results on April 24 indicated that the method failed to estimate the total sunlight and direct sunlight ratio. Reflectance and vegetation indexes obtained from different radiometric correction methods were all obviously affected by flight altitude. Furthermore, the variations of NDVI with flight altitude increasing were different with reflectance. Changes in reflectance and vegetation indexes with flight altitude had little effect on the correlation coefficients yielded with AGB, but showed a significant influence on those of LAI. Through analyzing the variation of observed solar radiation at different time intervals, caution is recommended when using the assumption that solar radiation is stable during the UAV flight. The longer the flight, the greater the variation in solar radiation, especially at sunrise and sunset. Even at noon, when the flight duration is 30 min, the change in solar radiation may exceed 10 % (e.g., 16.5 % on March 20).