A frequency measurement system for dual frequency He-Ne laser is set up based on a fiber femtosecond optical frequency comb and an external cavity diode laser. Using a Rb clock as a frequency standard, the diode laser that is locked to the optical frequency comb is traced to the Rb clock, and then the frequencies of the orthogonal polarized lasers are measured by beating with the locked diode laser at the same time. Locking the diode laser to the 1894449 th comb mode, the absolute frequency of the diode laser is 473612190000.0 ± 2.7 kHz, with a relative frequency uncertainty of 5.7×10-12. A commercial dual frequency He-Ne laser is measured to test the system, and the results show that the mean absolute frequencies of the horizontal polarized laser and the vertical polarized laser are 473612229934 kHz and 473612232111 kHz, respectively, with a relative Allan deviation of 5.2×10-11 at 1024 s, and the mean split frequency is 2.177 MHz with a standard deviation of 2 kHz.