Abstract: Objective The aim is to ensure reliability of the welding joint performance of 1000 MPa hydropower steel, providing theoretical and technical support for engineering applications. Methods The evolution law and mechanism of microstructure and properties of inter critical coarse grained heat affected zone of 1000 MPa hydropower steel under secondary thermal cycling are explored, the weak positions of welding heat affected zone performance are identified. The thermal simulation test machine is used to establish microstructure of heat affected zone and analyze mechanical properties of the samples. The performance differences of the heat affected zone under different thermal cycling conditions are compared through room temperature tensile test and −40 ℃ impact test. The microstructure, grain size and impact fracture morphology of the base material and heat affected zone are analyzed by scanning electron microscopy and metallographic microscope. Results The results show that the yield strength of fine grain heat affected zone is equivalent to that of coarse grain heat affected zone (980 Mpa±10 MPa), and both are higher than that of inter critical coarse grained heat affected zone (860 MPa). The tensile strength of fine grained heat affected zone and coarse grained zone is also comparable (1070 Mpa±10 MPa), both are higher than the inter critical coarse grained heat affected zone (931 MPa). The low temperature impact absorbed energy is highest in the fine grained heat affected zone (192 J), middle in the coarse grain heat affected zone (105 J), and worst in the inter critical coarse grained heat affected zone (62 J). Cnclusion Due to the coarsening of grains in the inter critical reheating coarse grained zone and partial austenitization of the original coarse grained heat affected zone structure, a mixed structure is formed after cooling. Compared with the fine grained heat affected zone, the initiation energy of inter critical coarse grained heat affected zone decreases by 24%, the expansion energy decreases by 81%, and the strength and impact performance are significantly reduced.