Leaf area index (LAI) and canopy chlorophyll content (CCC) are important indicators that describe the growth status and nitrogen deficiencies of crops. Several studies have been performed to estimate LAI and CCC using multispectral cameras onboard an unmanned airborne vehicle (UAV) system. However, the impacts of illuminations during UAV flight and problems of how to invert still need more investigation. UAV flights with a multispectral camera were performed under clear (diffuse ratio 0) and cloudy illumination conditions (diffuse ratio 1) over rapeseed, wheat and sunflower (only clear) fields. One-dimension radiative transfer model PROSAIL was run twice to generate a clear-sky model and a cloudy-sky model, respectively. The LAI and CCC of flights under a clear sky were inverted from the clear-sky model, and the flights under cloudy conditions were inverted from both clear-sky and cloudy-sky models to compare the results. Moreover, three Look-Up-Tables (LUT) were built with same input variables but different distributions of LAI. Results showed that LAI from uniform dense LUT had better correspondence with ground measurements for all crops (R2 = 0.51~0.69). The illumination condition had little impact on small to medium LAI (LAI < 5) and CCC. However, the inversion of imageries during cloudy sky conditions from the clear-sky model led to an overestimation of high LAI values.