Measurement of flow is crucial for assuring product quality, increasing manufacturing effectiveness, and promoting the development of science and technology. With the advancement of calibration and automation, standard devices using the mass method, volumetric method, and master meter method have limitations, such as low calibration efficiency and automation, large size, and complex operation. Innovations in this area are desperately needed. To realize the automation of calibrating ultrasonic water meters, a piston-type flow standard device calibration system with a high degree of automation, high calibration efficiency, small size, and easy operation was designed. A piston-type flow standard device was designed, the standard device was modeled, the selection of the main hardware and the design of the automated control of the hardware parts were completed; an automation control system adapted to the flow standard device was developed; and, furthermore, a water meter flow point calibration algorithm integrating the start–stop method and the dual-time method, as well as a water meter flow correction algorithm, was devised to improve the efficiency of ultrasonic water meter calibration. An uncertainty assessment of the designed system was completed; the standard uncertainty and expanded uncertainty of the device were 0.013% and 0.026%. Meanwhile, flow calibration tests were conducted, validating the rationality of the automated calibration algorithm for ultrasonic water meters. The results show that ultrasonic water meters calibrated with flow correction have a flow error within ±3% in the “low flow range” and within ±2% in the “high flow range”, with a repeatability of less than 0.05%. This indicates that a piston-type flow standard device, coupled with an automation calibration control system, can efficiently, accurately, and conveniently perform water meter calibration, and the system has good practical value.