The intercritical heat treatment process is considered a novel technology to solve the mismatch of strength and toughness of low alloy steel containing residual elements. In the present study, the effects of initial microstructure and intercritical quenching temperature on microstructural morphology, mechanical properties and fracture appearance of the experimental tin-bearing steel have been investigated. The results show that, under the same intercritical quenching and tempering (IQ-T) heat treatment parameters, the initial microstructures of bainite and ferrite (B-F) and complete martensite (M) yield different ferrite morphologies, block and strip-like ferrite, respectively. It is found that after IQ-T process, the tensile strength of the steel containing 0.09% tin with B-F as initial microstructure is 1061 MPa, but the impact energy value is only 26 J; while the steel with M has achieved the combined properties of high strength and excellent toughness, and the optimal intercritical quenching temperature is 770°C.