A protocol to realize complete and nondestructive atomic Greenberger–Horne–Zeilinger (GHZ)‐state analysis in cavity quantum electrodynamics (QED) systems is presented. In this protocol, the three information‐carrier atoms and the three auxiliary atoms are trapped in six separated cavities, respectively. After ten‐step operations, the information for distinguishing the eight different GHZ states of the three information‐carrier atoms is encoded on the auxiliary atoms. Thus, by means of detecting the auxiliary atoms, complete and nondestructive GHZ‐state analysis with high success probability is realized. Moreover, the driving pluses of operations are designed as a simple superposition of Gaussian or trigonometric functions by using the invariant‐based inverse engineering. Therefore, the protocol can be realized experimentally and applied in some quantum information tasks based on complete GHZ‐state analysis with less physical entanglement resource.