Thickness measurement of thin films is essential for quality control in the manufacturing process of the semiconductor and display industries. Real-time monitoring of film thickness during production is an urgent technical problem to be solved. In this study, a method for large-area thickness measurement of transparent films based on a multichannel spectral interference sensor is proposed. The sensor simultaneously acquires multichannel spectral interference signals through a combination of fan-out fiber optic bundles, detection probes, and an imaging spectrometer. The spectral data are calibrated and transformed into the wavenumber dimension, and then the power spectral density estimation method is used to demodulate the data frequency to swiftly derive the film thickness. The thickness measurement capacity of the proposed system is successfully validated on two standard film samples with a relative deviation of less than 0.38% and a relative standard deviation of less than 0.044%. The total spectral acquisition and calculation time for a single multichannel measurement was approximately 7.5 ms. The experimental results on polyimide films show that the measurement efficiency of the system is at least 4 times higher than that of the traditional system, indicating the potential of the multichannel spectral interference sensor for online monitoring in film production.