An accurate measurement algorithm of Doppler frequency rate between the clusters of pulses is given. The algorithm uses cross-correlating function between the succeeding pulse in the cluster to estimate ambiguous frequency of the cluster and select the same ambiguous frequency between the succeeding cluster of pulses to solve ambiguity to acquire the relative frequencies. Because these relative frequencies include the same ambiguity, the filter algorithm can be used to estimate the Doppler frequency rate between the clusters of pulses. The relative frequency and Doppler frequency rate estimation accuracy is high, and the process of solving the ambiguity is simple. The performance of the algorithm is effectively demonstrated by the computer simulation and ground test.