The accurate estimation of aboveground biomass (AGB) and leaf area index (LAI) is critical to characterize crop growth status and predict grain yield. Unmanned aerial vehicle (UAV) -based remote sensing has attracted significant interest due to its high flexibility and easiness of operation. The mixed effect model introduced in this study can capture secondary factors that cannot be captured by standard empirical relationships. The objective of this study was to explore the potential benefit of using a linear mixed-effect (LME) model and multispectral images from a fixed-wing UAV to estimate both AGB and LAI of rice. Field experiments were conducted over two consecutive years (2017–2018), that involved different N rates, planting patterns and rice cultivars. Images were collected by a compact multispectral camera mounted on a fixed-wing UAV during key rice growth stages. LME, simple regression (SR), artificial neural networks (ANN) and random forests (RF) models were developed relating growth parameters (AGB and LAI) to spectral information. Cultivar (C), growth stage (S) and planting pattern (P) were selected as candidates of random effects for the LME models due to their significant effects on rice growth. Compared to other regression models (SR, ANN and RF), the LME model improved the AGB estimation accuracy for all stage groups to varying degrees: the R2
increased by 0.14–0.35 and the RMSE decreased by 0.88–1.80 t ha−1
for the whole season, the R2
increased by 0.07–0.15 and the RMSE decreased by 0.31–0.61 t ha−1
for pre-heading stages and the R2
increased by 0.21–0.53 and the RMSE decreased by 0.72–1.52 t ha−1
for post-heading stages. Further analysis suggested that the LME model also successfully predicted within the groups when the number of groups was suitable. More importantly, depending on the availability of C, S, P or combinations thereof, mixed effects could lead to an outperformance of baseline retrieval methods (SR, ANN or RF) due to the inclusion of secondary effects. Satisfactory results were also obtained for the LAI estimation while the superiority of the LME model was not as significant as that for AGB estimation. This study demonstrates that the LME model could accurately estimate rice AGB and LAI and fixed-wing UAVs are promising for the monitoring of the crop growth status over large-scale farmland.