In recent years, for the structural characteristics and design requirements of the integral rotor and disc shaft of the integrated engine, the welding quality and mechanical properties of superalloy weldments have received increasing attention. In this paper, inertia friction welding (IFW) of FGH96 alloy was carried out using different welding parameters, and the homogeneous connection of FGH96 alloy hollow bars was successfully realized. The microstructure evolution, mechanical properties and fracture failure of the welded joints at room and high temperatures were investigated. The FGH96 alloy IFW joints were divided into the weld nugget zone (WNZ), the thermo-mechanically affected zone (TMAZ), the heat-affected zone (HAZ) and the base metal (BM), and there were significant differences in grain structure and distribution of the γ′ phase in each of the characteristic zones. The microhardness and tensile properties of the IFW joints were investigated, and the results showed an “M”-shaped curve in the microhardness distribution, with the lowest point of hardness observed in the HAZ. The tensile test results indicated that the fracture position moved from the BM to the WNZ with the increase in temperature, the microstructure at the fracture changed significantly and the tensile strength decreased from 1512.0 MPa at room temperature to 1201.3 MPa at 750 °C. The difference in the mechanical properties of the joints was mainly attributed to the changes in the dissolution and precipitation of the γ′ phase.