The traditional acquisition synchronization algorithm for spread spectrum security terminal had some shortcomings. This approach prolonged the security control processing time and failed to meet real-time requirements. The development of a high reliability and fast response synchronization algorithm is a key technology for the space-based TT&C receiver. To address this, a two-dimensional acquisition algorithm is employed, which is based on partial matched filtering assisted by inertial navigation + satellite navigation information and piecewise average FFT spectrum estimation. This conversion effectively reduces the Doppler frequency offset range and shortens the acquisition time. Additionally, the piecewise averaging 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 achieve high maneuverability and wide range tracking. An anti-false lock decision mechanism has been added to both the carrier tracking loop and pseudo code tracking loop to quickly escape from false lock states. Engineering applications have demonstrated that the use of 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 the real-time requirements.