This study explored the hydration reaction of ultra-high-performance concrete (UHPC) by using X-ray diffraction (XRD), nuclear magnetic resonance (NMR), and thermogravimetric analysis (TGA) as analysis methods. The partial- or no-known crystal structure (PONKCS) method was adopted to quantify the two main amorphous phases of silica fume and C-S-H; such quantification is critical for understanding the hydration reaction of UHPC. The measured compressive strength was explained well by the degree of hydration found by the PONKCS method, particularly the amount of amorphous C-S-H. During heat treatment, the pozzolanic reaction was more intensified by efficiently consuming silica fume. After heat treatment, weak but continuous hydration was observed, in which the cement hydration reaction was dominant. Furthermore, the study discussed some limitations of using the PONKCS method for studying the complicated hydration assemblage of UHPC based on the results of TGA and NMR. Generally, the PONKCS method underestimated the content of silica fume in the early age of heat treatment. Furthermore, the structural evolution of C-S-H, confirmed by NMR, should be considered for more accurate quantification of C-S-H formed in UHPC. Nevertheless, PONKCS-based XRD could be useful for understanding and optimizing the material properties of UHPC undergoing heat treatment.