The invention discloses a flowmeter calibration system with multiple calibration lines and a calibration method based on the system. The system comprises a water supply mechanism and a calibration mechanism, wherein the calibration mechanism comprises at least two standard tubes, all the standard tubes are connected with the water supply mechanism, a standard tube control valve and a standard flowmeter are installed on each standard tube, the water-out ends of all the standard tubes are connected with the same first converging tube, the first converging tube is connected with at least two calibration tubes, N to-be-detected flowmeters are connected in series on each calibration tube, a calibration tube control valve is also installed on each calibration tube, and all the calibration tubesare connected with the same flow regulation mechanism. According to the system, multiple calibration tubes are adopted and connected in parallel, multiple to-be-detected flowmeters are installed on each calibration tube, multiple to-be-detected flowmeters can be calibrated at a time when one arbitrary calibration tube is opened separately, different flowmeters can be calibrated when different calibration tubes are opened respectively, therefore, assembly-line calibration of the flowmeters is realized, and calibration time is greatly saved.