Thin-walled parts are widely used in aeronautical, aerospace and automotive applications due to their high performance-to-weight ratio. The thin walls in these parts also lead to low rigidity during machining, making them susceptible to deformation under the influence of the cutting force and/or the clamping force. As a result of spring-back effect after machining, significant machining error occurs in the thin-walled workpiece in its stress-free state. Analytical solution and FEM analysis of the deformation phenomenon are not robust against various machining conditions. To address this issue, a comprehensive error compensation scheme is proposed to predict and compensate for three major error sources, i.e. geometric error, thermal error, and force-induced error. The geometric and thermal errors of the machine tool are modeled and compensated to provide high motion precision for on-machine measurement. The force-induced error is obtained using on-machine measurement data. Comprehensive compensation of all three error sources is achieved by transforming individual compensation values into the same coordinate system. A real-time compensation system is developed based on the numerical control system of the machine tool. Compensation experiments carried out on two types of thin-walled parts show (i) a reduction of machining errors by at least 74% and (ii) an improvement of machining productivity by at least 41%, which validates the proposed compensation scheme.