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We discuss the Gaussian beam effect on the test of the equivalence principle using a free-fall interferometer.A two-lens assembly is used to improve the propagating character of the laser beam, and the beam radius is collimated to about 3.0 mm. The analysis shows that the gravity acceleration difference induced by the Gaussian beam effect could be less than 10-15 g for our double free-fall experimental design, but it would be 10-9 g for the absolute measurement of the gravity acceleration with the usual single free-fall method.