To overcome the poor sinterability and low fracture toughness of ZrC ceramics, a novel multi-scale microstructure design was proposed via a two-step in-situ reactive spark plasma sintering (SPS) process using ZrC, TiSi₂, and B₄C powders. During sintering, TiSi₂ preferentially reacted with B₄C to form TiB₂ and primary SiC, while the released Si further reacted with ZrC to yield ZrSi₂ and secondary SiC. The two-step SPS (1600 °C/3 min + 1800 °C/10 min) promoted complete in-situ reactions, liquid-phase sintering, and interdiffusion of Zr/Ti, leading to the formation of (Zr,Ti)C and (Ti,Zr)B₂ solid solutions. With the addition of 30 mol% TiSi₂ and 15 mol% B₄C, the multiphase ceramics exhibited a refined sub-microstructure (grain size < 500 nm), achieving a high flexural strength of 824 ± 46 MPa and fracture toughness of 7.5 ± 0.5 MPa·m^1/2. The synergistic enhancement in strength and toughness is attributed to a multi-scale strengthening/toughening mechanism: solid-solution strengthening at the atomic scale, effective grain boundary pinning by nano-sized primary and secondary SiC particles at the nano-scale, and toughening through crack deflection and bridging by TiB₂-SiC agglomerates and the higher-toughness ZrSi₂ phase at the microscale. This work provides a viable and innovative approach for designing high-performance ultra-high-temperature ceramics through tailored in-situ reactions and microstructural control.