Information on the spatial distribution of yields can be obtained over a large area by using remote sensing (RS) data. Combining Synthetic Aperture Radar (SAR), being sensitive to above ground biomass and soil moisture in all weather conditions, and optical data can improve the usability of RS data and provide a basis for pixel-based crop yield estimation (YE). In this study, an Upscaled Convolutional Gated Recurrent Unit model incorporated an attention mechanism (UpSc-AConvGRU model) was proposed to improve the estimation accuracy of the winter wheat growth parameter, Leaf Area Index (LAI). Gap filling the time series of optical data was done with backscatter coefficients, local incidence angles and polarimetric decomposition information from Sentinel-1 SAR imagery. The time series LAI estimated by the UpSc-AConvGRU model and Vegetation Temperature Condition Index (VTCI) retrieved from Sentinel-3 optical imagery were then used as state variables of the SAFY-V model to estimate winter wheat yield. The results showed that the proposed UpSc-AConvGRU model incorporated the Convolutional Block Attention Module (CBAM) can effectively improve the accuracy of LAI estimation, with RMSEs ranging from 0.413 to 0.699 m2 m2 for LAI estimated within main growth stages (MGSs) of winter wheat. The correlation between estimated LAI and Sentinel-3 retrieved LAI was generally higher at irrigated farmland compared to rain-fed farmland. The estimated LAI was closest to Sentinel-3 retrieved LAI at the green-up and late heading-filling stage of winter wheat, followed by the jointing and early heading-filling stage, and finally the milk maturity stage. There was good agreement between the SAFY-V model estimated and field measured winter wheat yields (R2 = 0.546, RMSE = 0.757 t ha−1), and the estimated yields at the pixel scale in the Guanzhong Plain, PR China were satisfactory. This study combined deep learning and crop growth modeling, proposed a new pixel scale winter wheat YE method.