An intrinsically stable quantum key distribution system (QKD) with six polarization states encoded by phase modulation is introduced. The encoder and decoder are in the same structures that consist of two polarizing Sagnac interferometers connected in tandem. The six polarization states are determined and distinguished by different sets of phase shifts induced by two respective electrically driven integrated phase modulators. A mean visibility of interference fringes is kept stable at 97.58% for an hours performance. Theoretical and experimental analyses show that the proposed QKD system features intrinsically stability immune from environment fluctuation.