Provided are a three-dimensional (3D) image acquisition apparatus, and a method of generating a depth image in the 3D image acquisition apparatus. The method may include sequentially projecting a light transmission signal, which is generated from a light source, to a subject, modulating reflected light, which is reflected by the subject, using a light modulation signal, calculating a phase delay using a combination of a first plurality of images of two groups, from among a second plurality of images of all groups obtained by capturing the modulated reflected light, and generating a depth image based on the phase delay.