In space-based TT&C receivers using spread spectrum system, the traditional acquisition synchronization algorithms for spread spectrum security terminal have extended security control processing times and failed to meet real-time requirements. Developing a high-reliability and fast-response synchronization algorithm is crucial. A two-dimensional acquisition algorithm is employed and it integrates partial-matched filtering, which bases on inertial and satellite navigation information, with piecewise average FFT spectrum estimation. By translating the motion status information reported by inertial and satellite navigation into Doppler frequency offset and Doppler frequency offset change rate estimation values, the Doppler frequency offset range is effectively reduced, the acquisition time is shortened, and piecewise average FFT spectrum estimation decreases the variance of power spectrum estimation. Furthermore, a second-order frequency-locked loop assisted by a third-order phase-locked loop is used in the carrier tracking loop to enhance maneuverability and tracking range. An anti-false lock decision mechanism in both the carrier and pseudo code tracking loops ensures quick escape from false lock states. Engineering applications demonstrate that this proposed algorithm results in a safety control processing delay of no more than 500 ms for the spread spectrum safety control terminal, thus meeting real-time requirements.