Based on the Fourier power spectrum theory, a measurement method by means of a random white-noise pattern transparent target was presented to analyze the effect of electron multiplication (EM)on the modulation transfer function (MTF) of electron multiplying charge-coupled device (EMCCD). By building an integrated system model of EMCCD, the multiplication MTFs at different multiplication gain were measured and discussed in experiments. The experimental results show that the electron multiplication process significantly influences the system MTF, compared with non-EM, especially at high EM gain. MTF declines by an average of about 30% at Nyquist frequency. The MTF and noise of auxiliary imaging optical system and the method of focusing judgment in experiment were also discussed.