In this paper, a self-compensation method for improving the accuracy of roll angle measurement of a linear stage caused by the non-parallelism of dual-beam due to time-dependent mechanical deformation of the support is proposed and integrated into a 5-DOF sensor to verify the feasibility. The non-parallelism between two laser beams is online real-time monitored by a pair of small autocollimator units. Through the ray-tracing analysis, the method to separate the roll angle of the moving stage and non-parallelism induced roll error is determined. A series of experiments under different supporting forces and ambient conditions have been carried out. The compensated P-V values of the roll angles are all within ±4 arc-sec, no matter how bad the originally measured value of the linear stage is. The average improvement of about 95% is significant. The effectiveness and robustness of the proposed measurement system in the changing environment are verified.