Accurate information of the fine-scale spatial patterns of trees and their interactions within a stand is critical for explaining the competition, health and vigor status, and future development of a stand. There are a number of indices which can show such patterns, but the stand spatial structure index is the most important. This index can be quantified based on the spatial information of trees (tree positions) within a stand and has paramount importance in identifying candidate trees to be thinned. This study develops a software tool (algorithm), which can conveniently and accurately estimate the stand spatial structure index. Our proposed algorithm considers the spatial relationships between a reference tree and its four adjacent trees, and computes the three most important stand structure indices (neighborhood comparison, uniform angle index and species mingling) using GIS (ArcEngine) and the C# programming language. The implementation of the developed algorithm (stand spatial structure index) shows that, for any reference tree assumed, its four adjacent trees identified by each of the three stand spatial structure indices (uniform angle index—UAI, mingling—M and neighborhood comparison—NC) are the same, indicating the consistency and accuracy between the three-stand spatial structural indices. For the same tree species in a forest stand, the computational results from each of the spatial structure indices used (UAI, M, NC) are also the same. Thus, the results of this algorithm developed in this study are consistent with that of the Winkelmass1.0 software (a type of software used to simulate stand spatial structure). As this article is based on the GIS technique, the computational results can be visually displayed and implemented on actual maps, making it more convenient and intuitive for forest management. The proposed approach will be useful for accurately identifying the trees to be thinned and helpful for maintaining the vigor stand structure. This study also demonstrates the implementation of the algorithm to the real-world data and proves that the computational process is simple and efficient. The application of this algorithm for the identification of trees to be thinned may help the stakeholders to focus their attention towards multi-functional forest management. The algorithm will also provide an important basis for optimizing thinning and maintaining well-structured forest stands.