To investigate the problem of small flow measurement, a micro Coriolis mass flowmeter is introduced which is designed with diversion pipe crossed. Liquid in two different tubes flows in the opposite direction. The measurement value of Coriolis mass flowmeter is the difference between the two tubes’ flow. A phase-frequency matching method for frequency estimation, phase difference estimation is discussed in detail. Smoothing method for the estimation results is also put forward. Experimental research is carried out under three different basic flows. On this basis, the zero stability, linearity and measurement error of the flowmeter are analyzed. The experimental results show that the zero point of the differential flowmeter has a great relationship with the basic flow. The instability of the zero point is estimated to be 0. 539 g / min, and the accuracy of the full range is within 0. 5%. The mass flow has a remarkable linearity with the time difference.