The atomic atmosphere and formation mechanism of the antiphase domain boundary (APB) may depend on the environmental variables of the phase transformation for the L12‐structural Ni3Al phase, which is the first important precipitate phase for Ni‐based superalloys. In this study, a discrete phase field method was used to reproduce the complete formation process of an APB without preset restrictions. Numerical calculations were performed to classify the atomic atmosphere, and its formation mechanism was revealed by calculating and analyzing the functional properties of the driving force. The formation process showed that four types of antiphase domains survived to form the APB. The numerical calculation results demonstrate that the atomic atmosphere has the same temperature dependence for hypo‐stoichiometric, stoichiometric, and hyper‐stoichiometric systems. However, Al plays two opposite roles in influencing the atomic atmosphere according to the changes in the alloy system. The positive and negative values of the driving force determine whether the atomic atmosphere is segregated or depleted, and the magnitude of the absolute value determines the atomic atmosphere level. This atomic‐scale study of nano‐scale ordered domain boundaries can provide theoretical information for further understanding of these and similar interfaces in ordered precipitation‐strengthened phases.This article is protected by copyright. All rights reserved.