Coral reef limestone differs greatly from common terrestrial compact rocks in terms of seepage characteristics due to its special pore structures. The high permeability causes reef limestone to have poor mechanical properties. Grouting is an effective approach to improve the mechanical properties of reef limestone, while the diffusion paths of grouts in reef limestone remain unclear. In view of this, a three-dimensional computerized tomography (CT) scanning system, a scanning electron microscope, a grout seepage system, and a laser particle-size analyzer were adopted to investigate the morphological characteristics of microscopic pores and the grout diffusion in reef limestone. Results show that four types of reef limestone (reef limestone built by Millepora platyphylla, reef limestone built by Goniopora gracilis, petaloid reef limestone, and reef limestone built by Astreopora myriophthalma) differ significantly in their microscopic pore structures. When pores are distributed uniformly, the grout diffuses in an I-shaped manner; if pores are distributed non-uniformly and growth lines are obvious, the grout diffusion pattern is mainly T-shaped. The transverse diffusion widths in the two diffusion patterns are highly correlated with the internal morphologies of reef limestone. In addition, the transverse diffusion width increases with time in the form of a power function. When grout diffuses in reef limestone, it first does so along cemented walls of pores, until reaching the ends of the fractures, where it then overcomes the bearing capacity of pore walls to flow from pores to the growth lines. Under the squeezing action of pores, the grout flows to the pores again from the growth lines (this process is then repeated). Moreover, the thicker the cemented walls of pores, the greater their influence over the grout diffusion path.