The invention discloses a method and a system for automatically controlling the ion implantation dose, which belong to the technical field of semiconductor manufacture. The method includes the following steps: acquiring the influence parameters of ion implantation dose in the manufacture process of a specific layer before the current layer, and getting the target implantation dose of the current layer through processing according to all the influence parameters and the standard implantation dose of an implantation process corresponding to the manufacture process of the current layer; comparing the target implantation dose of the current layer with a preset target dose range to determine a target dose range matching the target implantation dose; and selecting an ion implantation program corresponding to the determined target dose range, and determining the ion implantation dose in the manufacture process of the current layer according to the selected ion implantation program. The system is implemented according to the method. The technical scheme has the beneficial effect that the complexity of ion implantation dose automatic control is reduced, and the stability and safety of implantation dose adjustment are ensured.