In the frequency estimation of multi-segment signals, the error caused by discontinuity among different segments cannot be ignored. By correcting the phase difference of each segment, the results can be enormously improved, but the computational complexity of the algorithm grows on the same time. To resolve this problem, a new fusion algorithm based on spectrum zooming is proposed. The new algorithm performs spectrum zoom analysis to reduce the computational complexity while the precision is guaranteed, which is suitable to those real-time applications. Performance of the algorithm is demonstrated and analyzed through computer simulations.