Abstract: To address the martensitic hardening issue in the welding zone during the conventional rotary friction welding (RFW) of 40Cr and 45 steels, a novel process strategy of “low heat input rotary friction welding (LHI-RFW)” was proposed for dissimilar 40Cr/45 steel thin-walled tubes. Welding experiments were conducted by setting various combinations of LHI-RFW process parameters, and comparative analyses with the joints welded by the conventional process were carried out, including microstructure, welding temperature, and mechanical properties. The results indicate that the joint welded by the conventional process forms a hardened zone on the 40Cr steel side and a softened zone on the 45 steel side due to the high welding temperature; the novel LHI-RFW process strategy can significantly reduce the peak temperature at the welding interface, not only effectively suppressing the formation of hard and brittle martensite structure, but also avoiding the occurrence of microstructural softening. The test results of mechanical properties show that the tensile strength of the joint under the optimized process strategy reaches the level of the base metal; its bending property is superior to that of the joint welded by the conventional process.