Ti3SiC2 is recognized as a promising candidate material for nuclear energy applications; however, the microstructural defects resulting from complex irradiation processes remain elusive. This study investigates the microstructural evolution of Ti3SiC2 under sequential Xe-He-H ions irradiation at room temperature, followed by annealing at 900 °C, employing both experimental and first-principles computational approaches. A reverse phase transformation occurred following He irradiation, indicating that He facilitates the remote migration and recombination of Si vacancies through the formation of He-Si pairs during annealing. Post-annealing, the Xe-irradiated sample exhibited a widespread distribution of small Xe bubbles, whereas larger bubbles were prevalent at peak damage regions in the samples subjected to Xe+He and Xe+He+H irradiation. Concurrently, Si-rich precipitates with distinct distribution patterns were observed in samples irradiated with Xe, Xe+He, and Xe+He+H ions, significantly affecting the hardness. First-principles calculations reveal that the distinct damage profiles are primarily attributed to the dynamic behaviors of Si interstitials. The Ti-Si bonds are relatively weak and easily broken, leading to abundant Si interstitials in Xe ion irradiation, and He enhances Si diffusion. Conversely, H enhances Si segregation by preventing He from capturing Si interstitials. Within the TiC grains, He promotes Si migration, causing an approximately 700-fold increase in Si diffusivity at 900 °C. The Si segregation leads to the nucleation of 〈110〉 dislocation loops, culminating in the formation of distinctive strip-like Si clusters. This study elucidates the formation mechanism of Si segregation within Ti3SiC2, providing valuable insights for the design of irradiation-resistant materials.