We proposed a fast iterative algorithm for the multisection signals with the same length and known frequencydifference to increase precision and realtime performance of frequency estimation for multisection stationary signals while extending the applicable ranges of the existing methods. The algorithm includes the following technical features: The parameter matrix for frequencydomain analysis was generated to treat the unequal frequencies of different sections; The phasedifference compensation factor matrix was designed to obtain the frequency spectrum as well as the phasecontinuous signals; The search frequency sequence was generated to amend the unknown parameters in the phasedifference compensation factor matrix while obtaining the frequency spectrum amplitude matrix in a specific form; and, indirect iterative computation was adopted to improve the realtime performance of the algorithm. In addition, five important properties were given and proven to demonstrate the correctness of the algorithm. Simulated experiments were carried out under various complicated application environments. The results show good universality, noise immunity, realtime performance and better frequency estimation precision compared with the existing methods.