Coordinate transformation models often fail to account for nonlinear and spatially dependent distortions, leading to significant residual errors in geospatial applications. Here we propose a residual-based neural correction strategy, in which a neural network learns to model only the systematic distortions left by an initial geometric transformation. By focusing solely on residual patterns, the proposed method reduces model complexity and improves performance, particularly in scenarios with sparse or structured control point configurations. We evaluate the method using both simulated datasets with varying distortion intensities and sampling strategies, as well as under the real-world image georeferencing tasks. Compared with direct neural network coordinate converter and classical transformation models, the residual-based neural correction delivers more accurate and stable results under challenging conditions, while maintaining comparable performance in ideal cases. These findings demonstrate the effectiveness of residual modelling as a lightweight and robust alternative for improving coordinate transformation accuracy.