The invention provides a method and system for online prediction of macrosegregation in a continuous casting process, and the method comprises the steps: building a flow-heat transfer solidification-electromagnetism-mass transfer coupling three-dimensional model, and accurately calculating a macrosegregation result of a turbulence region in the continuous casting process; and then calculating a segregation result from the turbulence zone to the solidification tail end in the continuous casting process by taking a calculation result of an outlet of the turbulence zone as an initial condition ofa slicing model in a Profile form and by taking an interpolation method as an initial condition. The whole prediction process is automatically controlled through a self-programming program in combination with a TUI command stream, and operation is convenient. The method overcomes the defects of time and labor consumption and the like of the existing industrial experiment research mode, is greatlyhelpful for improving the internal quality of the casting blank, and also provides an important guiding effect for developing new variety steel at the same time.