The invention discloses a thin film thickness measurement method and system. The thin film thickness measurement system comprises a lighting optical device, an imaging optical device and a thin film thickness analyzing device, and is characterized in that the lighting optical device is used for generating a cone-shaped beam and projecting the cone-shaped beam to a point on the thin film surface of a sample; the imaging optical device comprises a focusing lens and an image acquisition module; the focusing lens projects light reflected from the surface of the sample to the image acquisition module according to the sequence of an incidence angle from small to large, the image acquisition module detects to acquire reflection intensity information of the beam at the surface of the sample and builds a relation curve between the reflectivity and the incidence angle according to the reflection intensity information; and the thin film thickness analyzing device builds a function of the reflectivity and a refraction angle cosine value by utilizing the relation curve between the reflectivity and the incidence angle and a Snell's law, and acquires the thin film thickness of the sample through performing Fourier transform and analysis on the function. The thin film thickness measurement system is not only high in measurement accuracy, but also simple, compact and stable in light path, low in cost and easy to realize online measurement.