The fraction of absorbed photosynthetically active radiation (FPAR), which represents the capability of vegetation-absorbed solar radiation to accumulate organic matter, is a crucial indicator of photosynthesis and vegetation growth status. Although a simplified semi-empirical FPAR estimation model was easily obtained using vegetation indices (VIs), the sensitivity and robustness of VIs and the optimal inversion method need to be further evaluated and developed for canola FPAR retrieval. The objective of this study was to identify the robust hybrid inversion model for estimating the winter canola FPAR. A field experiment with different sow dates and densities was conducted over two growing seasons to obtain canola FPARs. Moreover, 29 VIs, two machine learning algorithms and the PROSAIL model were incorporated to establish the FPAR inversion model. The results indicate that the OSAVI, WDRVI and mSR had better capability for revealing the variations of the FPAR. Three parameters of leaf area index (LAI), solar zenith angle (SZA) and average leaf inclination angle (ALA) accounted for over 95% of the total variance in the FPARs and OSAVI exhibited a greater resistance to changes in the leaf and canopy parameters of interest. The hybrid inversion model with an artificial neural network (ANN-VIs) performed the best for both datasets. The optimal hybrid inversion model of ANN-OSAVI achieved the highest performance for canola FPAR retrieval, with R2 and RMSE values of 0.65 and 0.051, respectively. Finally, the work highlights the usefulness of the radiation transfer model (RTM) in quantifying the crop canopy FPAR and demonstrates the potential of hybrid model methods for retrieving the canola FPAR at each growth stage.