Abstract: Aiming at the characteristics of 1 GHz bandwidth Chirp transform spectrometer with high time resolution and narrow pulse width, as well as the demand for detection of weak signals, a real-time and high-precision back-end timing synchronization and pulse accumulation scheme for CTS system is proposed, which also has the advantage of adjustable integration time. The scheme achieves the synchronization control between the analog and digital parts of the 1 GHz bandwidth CTS system and the precise accumulation of 1 ns narrow pulse in the back-end through system clock design and FPGA algorithm design, in order to ensure that the system achieves a high frequency resolution. Through this synchronization scheme, The average in-band pulse width of the system after accumulation is 1.0136 ns, and the corresponding frequency resolution is 101.36 kHz, which is comparable to the resolution of the CTS carried by the JUICE of ESA, and provides an effective solution to realize the high-precision spectrum analysis of China's deep-space exploration mission.