This paper proposes a method of using diffraction phase microscopy combined with microfluidic chip to quantitatively measure waterborne parasites. A diffraction phase microscopy system is built up by combining interferometry with optical microscope to achieve high sensitivity real-time measurement of parasites. Based on soft lithographic techniques, a double-layered microfluidic chip with U-shaped trapping structures is designed and fabricated for high throughput single parasites trapping. Ficoll solution with the same refractive index as polydimethylsiloxane (PDMS) is introduced into the microfluidic chamber to eliminate significant artifacts in phase imaging originating from diffraction at the edges of trapping structures. The accuracy of the system is verified using standard polystyrene microspheres of different diameters, and the error of maximum phase shift does not exceed 3%. 100 Giardia Lamblia (G. Lamblia) cysts and 100 Cryptosporidium Parvum (C. Parvum) oocysts are measured using this system. The phase maps of the parasites are obtained from the interferograms. The morphological parameters and quantitative optical volume difference distribution of the two kind of waterborne parasites are obtained by analyzing the quantitative phase maps. Quantitative data provides the basis for understanding their physiological characteristics. The microfluidic diffraction phase microscopy system has simple structure, good stability and high measurement accuracy, and has great potential for real-time monitoring and label-free quantitative studies of single microorganism.