The setting time of the paste and the rheological properties and microstructure of the mortar after replacing OPC cement with silica fume (SF), fly ash cenosphere (FAC) and nano-silica are studied as a reference for shotcrete applications. The suggested contents of SF, FAC and nano-silica are around 5–7.5%, higher than 20% and 1–3%, respectively, to meet the initial setting time specification. Viscosity and yield stress of mortar are highly dependent on water/cement ratio and paste/sand ratio. At the higher water/cement ratio, viscosity is more based on the paste itself. For SF of 2.5–10%, viscosity and yield stress increase, and the flowability of the mixture decreases. For FAC of 5–25%, viscosity and yield stress increase with a lower rate than SF, and flowability increases at 5% and then decreases as FAC content increases, which, however, is at the same level as the control. When SF and FAC are both added, a tortuous behavior of viscosity is shown. As nano-silica is further added, significant increases in viscosity and yield stress are shown. The compressive strengths of mortar with different supplementary cementitious materials (SCMs) at early ages are close. The difference in compressive strength after 28 days of standard curing is significant. The SF5-FAC15 group exhibits the largest increase in strength for 32.82%. At the age of 2.5 h, the macropore areas distribution of SF5-FAC25-NS1.5 test groups were 31.96%, indicating the lowest macropore area distribution. The secondary hydration reaction of supplementary cementitious materials (SCMs) continuously generates products that fill the pores, and the ultrafine filling effect of nanomaterials improves the compactness of the mortar microstructure and reduces the macropore area distribution. The mercury intrusion test results of the SF5-FAC25-NS1.5 group show that the pores are concentrated within the range of 0.01 to 0.05 μm, and the most probable pore size is significantly smaller than that of the CTR group. As the overall replacement level of SCMs increases, the diffraction peak of calcium hydroxide gradually weakens.