Microstructure difference between the center and the surface caused by temperature gradient during quenching process may lead to inhomogeneous properties of large-size products. A new finite element model (FEM) is proposed in the present work to precisely simulate temperature distribution of a bainite/martensite multiphase material during water-air alternating surface quenching process. Parameters like nonlinear variation of thermo-physical parameters, nonlinear variation of heat transfer coefficient, phase transformation latent heat, and transformation kinetics were considered when developing the FEM. In particular, the experimental investigation of bainite and martensite transformation kinetics provides the basis for the accurate calculation of microstructure. The model helps identify the temperature distribution, cooling rate profile, microstructure and hardness characteristic of Mn-Si-Cr bainitic/martensitic large-size products. A quarter of axle block experiments were conducted to validate the proposed FEM, which shows high precision. The error of simulated temperature was lower than 5 % and that of hardness was within 2 %. Then, the model is used to simulate the discrepancy between surface and center location under as-employed quenching. Both experiment and simulation results confirmed that the different cooling rate leads to the temperature gradient. Different temperature distribution resulted in inhomogeneous properties of large-size product. Effects of the intensity of water spraying on large-size product are compared thoroughly in the simulation analysis. It is reflected that the improvement of microstructure and corresponding diminution of non-uniformity in hardness can be realized through optimizations of key processing parameters. Therefore, it is helpful for quenching process design of large-size products.