Atomic thickness thin films are critical functional materials and structures in atomic and close-to-atomic scale manufacturing. However, fast, facile, and highly sensitive precision measurement of atomic film thickness remains challenging. The reflected light has a dramatic phase change and extreme reflectivity considering the Brewster angle, indicating the high sensitivity of the optical signal to film thickness near this angle. Hence, the precision polarization measurement method focusing on Brewster angle is vital for the ultrahigh precision characterization of thin films. A precision polarization measurement method based on a liquid crystal variable retarder (LCVR) is proposed in this paper, and a measurement system with a high angular resolution is established. A comprehensive measurement system calibration scheme is also introduced to accommodate ultrahigh precision film thickness measurement. Repeatable measurement accuracy to the subnanometer level is achieved. Standard silicon oxide film samples of different thicknesses were measured around Brewster angle using the self-developed system and compared with a commercial ellipsometer to verify the measurement accuracy. The consistency of the thickness measurement results demonstrates the feasibility and robustness of the measurement method and calibration scheme. This study also demonstrates the remarkable potential of the LCVR-based polarization method for atomic film thickness measurement in ultraprecision manufacturing.