The accuracy of flow measurement has become increasingly demanding with the rapid development of modern industry. Therefore, the high-precision measuring is very important for the flow liquid in the soft design and the hardware equipment. Since traditional flow-meter is difficult to filter out data errors, we propose a frequency-domain filtering of the data processing algorithm and design a complete high-precision measuring system based on the measuring principle of non-contact-type time difference ultrasonic flow-meter. The real-time data signal is collected using the high-precision measurement chip named TDC-GP2, which is perfectly suited for ultrasonic flow-meter and heat-meter applications. Then the processing algorithm realized on microprocessor chip and filters error signal. After simulation and field tests the results show that the flow-meter has better accuracy and linearity. The algorithm meets the demands in the accuracy of measuring results. There will be great prospects on the flow measurement and real-time flow of flow-meter.