Polycarboxylate superplasticizer (PCE) is a key ingredient in the preparation of ultra-high performance concrete (UHPC). However, it is still unclear how PCE affects hydration and microstructure evolution of UHPC, and how it changes the rheological properties over time. In this paper, the rheological properties in the early 5 h were measured by rotational and oscillatory shear tests, and solid and liquid phase composition were analyzed by thermogravimetric analysis, atomic emission spectrometer and 1H nuclear magnetic resonance relaxation method (1H NMR). The results show that the free water content in fresh concrete decreases with time, and the particle void shrinks, resulting in a smaller space for water distribution. As the particle void decreases from 139.89 nm to 121.665 nm, the plastic viscosity and storage modulus increases rapidly, and the mixture loses fluidity when average void size is less than 105.825 nm. After increasing the content of PCE in UHPC, the formation of early hydration products was inhibited, and the shrinkage of particle void in the slurry slowed down, leading to the decreasing of the plastic viscosity of UHPC over time.