When Moiré tomography is applied to measure the temperature of complex flow fields, a partition reconstruction method is used to minimize the influence of species composition on the results obtained, which is essential to ensure measurement accuracy. Considering the complexity of flow field structures, a boundary searching algorithm is proposed in this study to automatically divide the regions of the measured high-temperature complex flow fields. A propane-air flame and an argon arc plasma are used to verify the feasibility of the proposed algorithm. The results show that this algorithm can simultaneously improve the calculation efficiency and accuracy of boundary search in the divided flow field regions. This study provides a foundation for widening the range of applications of Moiré tomography.