Aboveground biomass (AGB) directly reflects crop carbon fixation capacity. Utilizing unmanned aerial vehicle (UAV) remote sensing for high-throughput AGB monitoring offers benefits to agricultural management and food production. This study aimed to develop a method for monitoring AGB in film-mulched crops using UAV multispectral data. A three-year field experiment was conducted using wheat (Exps. 1 and 2 in 2021–2022, and Exps. 5 and 6 in 2022–2023) and maize (Exps. 3 and 4) with varying cropping patterns. Spectral indices (SIs) of different feature reflectances (e.g., vegetation, soil, and mulch pixels) were reconstructed using least absolute shrinkage and selection operator methods. The Bayesian model averaging (BMA) method integrated seven independent machine learning algorithms to construct a Bayesian ensemble model (BEM). The results demonstrated that spectral index reconstruction (SIR) enhanced the correlation between SIs and AGB, while BMA reduced model uncertainty and improved AGB prediction accuracy. The BEM model, based on Exps. 1 and 2 datasets, achieved determination coefficients of 0.78–0.84 and root mean square error (RMSE) of 0.81–0.89 t ha−1. Model validation across years and crops demonstrated the generalization of the SIR + BEM method for AGB estimation. The RMSEs of the model inter-annual transport predictions were 0.83 and 0.93 t ha−1 in Exps. 5 and 6, respectively, and RMSE of the predictions between crops was 1.43 t ha−1 for the maize dataset (Exps. 3 + 4). The approach proposed in this study has great potential for monitoring growth status of film-mulched crops at the farm scale and providing guidance for precision agriculture management.