The invention discloses an arbitrary waveform generating system based on a user-defined processor. In a control portion, a waveform generating module generates various waveform segment data downloaded to a hardware portion through a waveform downloading module, a control program generating module receives an externally inputted instruction set, and the instruction set is downloaded to the hardware portion after compiling of a compiling module. In the hardware portion, a storage control logic module controls reading and writing of a waveform memory, the user-defined waveform processor receives and analyzes the instruction set, generates call instructions for corresponding waveform segments according to names of the waveform segments indicated by the instruction set, transmits the call instructions to the storage control logic module and receives the waveform segment data read by the storage control logic module, and analog signals are outputted after combined waveform segment data are conditioned according to the call sequence and the call frequency of the waveform segment indicated by the instruction set. By the aid of the arbitrary waveform generating system, data transmission time of the control portion and the hardware portion during waveform generation can be shortened.