Pore structure, the most important structural feature of reactive powder concrete (RPC) with nanofillers, is closely related to the dispersion quality, content level and internal structure of nanofillers. In order to characterize the pore structure of RPC and comprehensively understand the effect of nanofillers on the microscopic behavior of concrete, this paper studies the pore structure of RPC containing different types (including zero-dimensional nanoparticles, one-dimensional nanotubes and two-dimensional nanosheets) and content (0.25-3%) of nanofillers by using low-field nuclear magnetic resonance. The experimental results show that incorporation of all types of nanofillers reduces the porosity of RPC and causes shrinkage of gel pores and fine capillary pores. Among different types of nanofillers, one-dimensional nanotubes are most beneficial to reduce porosity, and zero-dimensional nanoparticles have a more pronounced effect on reducing pore size. The effect of nanofillers on the pore structure of RPC is mainly attributed to the conversion of pore water inside C-S-H gel, inducing reorganization of gel structure. Specifically, nanoparticles cause the gel layer surrounding the pore water to shrink or even partially collapse, while nanotubes and nanosheets fill the collapsed gel layers with pore water, in turn, producing a slight swell between gel layers. It is the slight changes in the microstructure of C-S-H gel that cause shrinkage and deformation of concrete materials at the macroscopic scale, which, in turn, greatly affects the overall performances of RPC with nanofillers.