Linear friction welding (LFW) technology, as an advanced manufacturing approach to fabricate the bimetallic turbine blisks, is receiving increasing attention from aerospace industries. Current work experimentally investigated the microstructural evolution and microhardness in LFW of FGH4096 and GH4169 superalloys. A complete dynamic recrystallization (DRX) was obtained in friction interface zone (FIZ) with no obvious secondary phases including δ and carbide phases on GH4169 side, and primary and secondary γ′ phases on FGH4096 side. The thermal-mechanically affected zone (TMAZ) was characterized by incomplete DRX where a significantly lower amount of low angle grain boundaries existed together with partially dissolved secondary phases depending upon the distance from weld line. The above-mentioned distinct microstructural behavior, manifesting different thermo-mechanical fields at different areas in the joint, necessitated the further analysis of numerical simulations of LFW of two dissimilar alloys. A thermo-mechanical coupling model was developed to predict the temperature, plastic strain and stress distributions. Satisfactory comparisons between numerical and experimental results were observed. The findings in the work are believed to be one of few currently available to focus on the study of metallurgical and thermo-mechanical coupling behavior of the dissimilar nickel-based superalloy joint made by the LFW process.