Soil moisture content (SMC), as a pivotal component in the energy and matter exchange processes within the soil-plant-atmosphere continuum, plays a crucial role in surface water dynamics, energy fluxes, and carbon cycling within ecosystems. The development of remote sensing technology has offered new perspectives for monitoring soil moisture at regional scales. Unmanned aerial vehicles (UAV) equip with multispectral remote sensing technology have distinct advantages for vegetation monitoring at the field scale, including rapidity and cost-effectiveness, which has superior applicability and practicality at the field scale. Therefore, in a 5a "Daya" late-maturing citrus orchard, the vegetation index (VI) and texture feature (TF) information of citrus canopy based on UAV multi-spectral images as well as soil and plant analyzer development (SPAD) of citrus physiological parameter were extracted. These different data sources were integrated into the framework of the random forest algorithm (RF) and genetic algorithm-optimized random forest (GA-RF) to evaluate the accuracy of surface SMC (SSMC) estimation in citrus orchard. The Biswas model was utilized to simulate the root zone SMC (RSMC) in citrus orchard. The spatiotemporal variations of soil moisture in citrus orchards were analyzed, and the potential of low-cost sensor-equipped drones in rapidly acquiring spatial and temporal distribution information of soil moisture at a large regional scale was explored. The results indicated that the GA-RF model outperformed the RF model in estimating citrus orchard SMC (with R2 ranging from 0.502 to 0.949 and RMSE ranging from 0.552 to 3.166% for GA-RF, compared to R2 ranging from 0.430 to 0.936 and RMSE ranging from 0.587 to 3.449% for the RF). The GA-RF model using VI+SPAD as inputs exhibited the best performance for SMC at depths of 5cm, 10cm, 20cm and 40cm (SMC5, SMC10, SMC20 and SMC40) across four citrus growth stages (R2 ranging from 0.793 to 0.949 at 5cm, R2 ranging from 0.702 to 0.938 at 10cm, R2 ranging from 0.714 to 0.927 at 20cm). In bud bust to flowering, young fruit and fruit maturation stages (stage Ⅰ, ⅠⅠ and ⅠⅤ), all models demonstrated good accuracy in estimating SMC at depth of 10cm (R2 ranging from 0.567 to 0.908 in stage Ⅰ, with R2 ranging from 0.681 to 0.916 in stage ⅠⅠ and R2 ranging from 0.579 to 0.938 in stage ⅠⅤ). In fruit expansion stage (stage III), the models performed best in predicting SMC5 (R2 ranging from 0.698 to 0.861). The Biswas model was constructed to simulate SMC40 by utilizing the inverted SMC10 and SMC20, thereby generating spatiotemporal distribution maps of SMC at different depths in citrus orchard. The SSMC was susceptible to environmental factors, exhibiting significant spatiotemporal heterogeneity. In summary, this study illustrated that the integration of multiple data sources into GA-RF model enhanced the estimation performance of SMC at different growth stages of late-maturing citrus orchards in the Southwest China. Additionally, it enabled the rapid and efficient monitoring of spatiotemporal variations in SMC, providing an effective method and practical foundation for precision irrigation and improved water use efficiency in agricultural fields.