Ultra-high-performance concrete (UHPC) made of limestone calcined clay cement (LC³) exhibits excellent mechanical properties as well as good environmental friendliness. This paper studied the improving effect of nano-SiO₂ on the mechanical properties and microstructure of LC³-UHPC. The experimental results show that the addition of nano-SiO₂ demonstrates obvious advantages. The mechanical properties of LC³-UHPC are enhanced, and the frictional bond performance between steel fiber and cementitious matrix is also improved. The fiber/matrix bond strength is increased. A constitutive model describing the single fiber pullout behavior is established, and the values of related parameters are suggested. Besides, nano-SiO₂ also refined the cementitious microstructure of UHPC and made the matrix denser. Based on the comprehensive analysis of mechanical properties and microstructural characteristics, the optimal content of LC³ and nano-SiO₂ were proposed.