A simple microwave photonic, reconfigurable, instantaneous frequency measurement system based on low-voltage thin-film lithium niobate on an insulator phase modulator is put forward and experimentally demonstrated. Changing the wavelength of the optical carrier can realize the flexibility of the frequency measurement range and accuracy, showing that during the ranges of 0–10 GHz, 3–15 GHz, and 12–18 GHz, the average measurement errors are 26.9 MHz, 44.57 MHz, and 13.6 MHz, respectively, thanks to the stacked integrated learning models. Moreover, this system is still able to respond to microwave signals of as low as −30 dBm with the frequency measurement error of 62.06 MHz, as that low half-wave voltage for the phase modulator effectively improves the sensitivity of the system. The general-purpose, miniaturized, reconfigurable, instantaneous frequency measurement modules have unlimited potential in areas such as radar detection and early warning reception.