A high sensitivity atom flux sensor based on atomic absorption spectroscopy has been designed and implemented to control electron beam evaporators and effusion cells in a molecular beam epitaxy system. Using a high-resolution spectrometer and a two-dimensional charge coupled device detector in a double-beam configuration, we employ either a non-resonant line or a resonant line with low cross section from the same hollow cathode lamp as the reference for nearly perfect background correction and baseline drift removal. This setup also significantly shortens the warm-up time needed compared to other sensor technologies and drastically reduces the noise coming from the surrounding environment. In addition, the high-resolution spectrometer allows the most sensitive resonant line to be isolated and used to provide excellent signal-to-noise ratio.