Based on the Schrdinger equation for atomic waves, the relation between the gravity and the phase difference of atom interferometer is derived. A new 3×3 matrix method was introduced to calculate the phase difference for complicated system of the multiloop interferometers, which simplifies the calculation greatly. By use of this method, not only the propagation matrix of atom beam in free space under the influence of gravity can be, but also the interaction matrix of atom beam with π/2 and π pulse can be obtained. As an example, the phase difference for the three-pulse atom gravimeter by using the 3×3 matrix is derived, and the results obtained coincide precisely with those obtained by Wolf et al. through the integration of the Lagrangian over the classical trajectory. Finally, the phase difference of five-pulse atom gravimeter is analyzed to illustrate the convenience of the 3×3 matrix method.