The invention discloses a quantum key distribution system based on a reference system independent protocol. A photo-injection semiconductor laser is adopted to generate a quantum state with coded information, which replaces a traditional scheme of a light source and quantum state coding module. Time and phase difference information of photons is generated by the photo-injection semiconductor laser in a quantum key encoder end; a first laser driver, a second laser driver, a pulse generation laser, a phase preparation laser and a first three-port circulator in the quantum key encoder end form the photo-injection semiconductor laser; and the second laser driver controls the phase preparation laser to inject a phase modulation optical pulse with a preset delta phi phase into the pulse generation laser, so as to enable the pulse generation laser controlled by the first laser driver to generate a pair of double-pulse signal light with a phase difference of delta phi, thereby generating a pulse sequence with time and phase coded information. The technical scheme of the invention improves the anti-interference performance and the code rate of the system, and is favorable for the integration and miniaturization of products.