Lasers with compact size, low cost and low noise are desirable for developing practical non-classical sources. Compared with Tisapphire mode-locked laser, Yb-doped photonic crystal fiber (PCF) based mode-locked laser has the advantages of simple structure, compact size and low cost, but its noise characteristics need to be further investigated. The noise of an Yb-doped PCF based femtosecond laser is measured and analyzed by a home-made self-homodyne detection system which is suitable for measuring the noise of pulsed laser. The results show that the amplitude noise of the PCF based laser is much higher than that of the shot noise level, which means that the output of the laser is not in the ideal coherent state, and its noise characteristics should be further improved.