A series of cerium phosphate catalysts with different crystal phases were synthesized by hydrothermal method and co-precipitation method. Hexagonal cerium phosphate (CePO4-H) shows better NH3-SCR denitration activity than monoclinic cerium phosphate (CePO4-M) and mixed phases of CePO4-H and CePO4-M. Moreover, CePO4-H also exhibits excellent activity stability with stream time and cycling stability. Various characterizations were carried out to explain the effects of different crystal phases of CePO4 on the activity. Among these catalysts, CePO4-H has much stronger surface acidity that is conducive to the adsorption and activation of NH3, and more surface adsorbed oxygen species that can effectively improve SCR activity. In situ diffuse reflectance infrared Fourier transform spectroscopy (DRIFTS) were performed to investigate the adsorption and reaction of NH3 and NOx on CePO4-H and CePO4-M, and the results suggest that the better activity over CePO4-H follows mainly the Eley–Rideal mechanism in the activity temperature window (300–500 °C) with 100% NO conversion.