The invention discloses a perpendicular coupling nanometer optical waveguide dual-optical-path chip atomic clock which comprises a laser, light beams emitted by the laser enter a Y waveguide beam splitter through coupling of a perpendicular coupling optical grating I, one beam of light is output after passing by a phase modulation unit, another beam of light is output after regulation compensation, the two beams of light are output after passing by the perpendicular coupling optical grating I and a perpendicular coupling optical grating II respectively, enter a rubidium atom air chamber after passing by a polarizing film, an attenuation plate and a wave plate and after collimation and focussing and are input into an integrated circuit chip by a subtracter after emitted and converted into electrical signals by a detection unit, and the integrated circuit chip controls the laser and the phase modulation unit. According to the scheme, luminous power fluctuation and frequency fluctuation noise influences can be reduced greatly through dual-optical-path common-mode rejection, the signal-to-noise ratio of a CPT atomic clock is effectively improved, and accordingly, the short period stability of a chip level atomic clock can be improved greatly.