This study explores the effects of metakaolin (MK) and silica fume (SF) on rheological behaviors and microstructure of self-compacting concrete (SCC). The rheology, slump flow, V-funnel, segregation degree (SA), and compressive strength of SCC are investigated. Microstructure characteristics, including hydration product and pore structure, are also studied. The results show that adding MK and SF instead of 4%, 6% and 8% fly ash (FA) reduces flowability of SCC; this is due to the fact that the specific surface area of MK and SF is larger than FA, and the total water demand increases as a result. However, the flowability increases when replacement ratio is 2%, as the small MK and SF particles will fill in the interstitial space of mixture and more free water is released. The fluidity, slump flow, and SA decrease linearly with the increase of yield stress. The total amount of SF and MK should be no more than 6% to meet the requirement of self-compacting. Adding MK or SF to SCC results in more hydration products, less Ca(OH)₂ and refinement of pore structure, leading to obvious strength and durability improvements. When the total dosage of MK and SF admixture is 6%, these beneficial effects on workability, mechanical performance, and microstructure are more significant when SF and MK are applied together.