The invention discloses a two-shaft numerical control system and a tool overload protection method, wherein the two-shaft numerical control system comprises an upper computer and a lower computer which are connected through a bus, the upper computer comprises an ARM embedded single chip computer, a USB interface module, a display and a keyboard, the USB interface module, the display and the keyboard are respectively connected with the ARM embedded single chip computer through a wire, the ARM embedded single chip computer is internally provided with a G-code file editing, reading and storing module, the lower computer comprises two ARM embedded single chip computers internally provided with G-code analysis modules, each of the two ARM embedded single chip computers is connected with an I/O interface and an execution unit, three observed values, namely a motor load observed value, a displacement observed value and a rotating speed observed value, of a main shaft tool are taken as an input of an off-line training SVM classifier, the overload condition of a main shaft motor is taken as an output, so that the overload condition of the main shaft motor is recognized. The two-shaft numerical control system is flexible to machine; overload protection of a tool is realized.