In this paper, combined with the advanced controlled rolling and cooling process represented by 2250mm hot continuous rolling production line in China, an on-line heat treatment process (DQ&P&T) is developed, which uses dense laminar flow cooling to conduct sectional quenching, isothermal distribution and low-temperature coil taking from tempering after rolling, and a comparative analysis were made with the traditional off-line quenching and tempering heat treatment process (RQ&T) to produce rare earth microalloyed ultra-high strength steel (Rm≥1200MPa). By means of optical microscope, scanning electron microscope, equipped with electron backscatter diffractometer, tensile testing machine, impact testing machine, Vickers and wet sand/rubber wheel wear testing machine, the microstructure transformation morphology and mechanical properties of the test steels under two heat treatment systems were systematically analyzed. The results show that the microstructure of the test steels at room temperature are composed of lath martensite, bainite ferrite and a small amount of residual austenite under the two heat treatment processes. Compared with off-line heat treatment (RQ&T), the lath martensite content of the steel tested by on-line heat treatment (DQ&P&T) is decreased and the bainite ferrite content is increased. The bainitic ferrite formed by isothermal transformation interposed and divided the deformed undercooled austenite, which promotes the refinement of the grain size and the increase of the proportion of large angle grain boundaries, and improves the strength, toughness and wear resistance of the material, however, the uniformity of hardness in the thickness direction of the product is inferior to that treated by RQ&T process. Relative to off-line heat treatment, the on-line heat treatment has higher efficiency and lower manufacturing cost in the production of high strength steel, and the performance of the product meets the standard requirements, which proves that online heat treatment process is feasible.