In order to improve precision and dynamic response speed of the correlation method for phase difference measurement under the asynchronous sampling circumstance, an improved method for phase difference measurement based on correlation theory is proposed. Firstly, two reference signals which have 90 phase shifted are introduced by using two original signals with the same frequency, then, via digital filter with zero phase, correlation function of the original signals and reference signals are directly computed, some properties about correlation and sine function are adopted to obtain the computational formula for phase difference. Theory analyses and experiment results show that it is not necessary for the proposed algorithm to know the signal frequency in advance, and the measuring accuracy for this method is not affected by whether synchronous sampling or not, it can also measure the dynamic phase difference. Compared with the traditional methods, it is superior to accuracy, robustness and universality.