A bainite/martensite multiphase rail is treated by the controlled-cooling process with different finish-cooling temperatures. The simulated temperature–time curves of the position of 5 mm and 15 mm below the rail tread (P5 and P15) express different trends. P5 has greater impact toughness and lower tensile strength than P15. Microstructural characterization was carried out by conducting scanning electron microscopy, X-ray diffraction, electron backscatter diffraction, and transmission electron microscopy. The greater tensile strength is due to the dispersed ε-carbides hindering the movement of dislocations. The greater impact toughness is attributed to the filmy retained austenite and the smaller effective grain with high-angle boundary. Finite element modeling (FEM) and microstructural characterization reasonably explain the changes of mechanical properties. The present work provides experimental and theoretical guidance for the development of rail with excellent mechanical properties.