This paper proposes an effective compression method to utilize the 3D integral image with large amount of data obtained by a lens array in various applications. The conventional compression methods for still images exhibit low performance in terms of coding efficiency and visual quality, since they cannot remove the correlation between elemental images. In the moving picture compression methods, 1D scanning techniques that produce a sequence of elemental images are not enough to remove the directional correlation between elemental images. The proposed method effectively sequences the elemental images from an integral image by the 2D referencing technique and compresses them using the multi-frame referencing of H.264/AVC. The proposed 2D referencing technique selects the optimal reference image according to vertical, horizontal, and diagonal correlation between elemental images. Experimental results show that compression with the sequence of elemental images presents better coding efficiency than that of still image compression. Moreover, the proposed 2D referencing technique is superior to the 1D scanning methods in terms of the objective performance and visual quality.