Soil moisture content is a vital variable in agricultural, hydrological, ecological and climatological processes. However, susceptible to soil type, soil structure, topography, vegetation and human activities, soil moisture content exhibits strong spatial heterogeneity in spatial distribution, which makes it difficult to accurately estimate the soil moisture content distribution information at a large scale using conventional methods. To solve the problem, this study proposed a novel hybrid model (PSO-LSTM) based on the particle swarm optimization (PSO) and long short-term memory (LSTM) network model to accurately predict soil moisture content at a large scale. Five different input combinations were constructed based on the vertical polarization (VV) and cross-polarization (VH) of multi-phase Sentinel-1A data, and the soil moisture content at depths of 5 cm, 10 cm, 20 cm and 40 cm in citrus orchards were estimated using the standalone LSTM and hybrid PSO-LSTM models. The results showed that the estimation accuracy of the hybrid PSO-LSTM model was greater than that of the standalone LSTM model at different depths, with the normalized root mean square error (NRMSE) of 4.568–11.023 % and 18.056–30.156 %, respectively. With the VV polarization as the only inputs, the PSO-LSTM model obtained high prediction accuracy, with the normalized root mean square error (NRMSE) of 5.458–10.125 %, respectively. Therefore, the PSO-LSTM model with VV polarization input was recommended to estimate the soil moisture content at different depths in citrus orchards, which provides important data for decision-making on distributed precision irrigation at a large scale.