As a supplement to the traditional community structure index system, eco-exergy is applied to forest ecosystems to quantify the bio-thermodynamic spatial structure of the community by measuring the genetic information contained in the species, and to measure and evaluate the stability and health of the community. Based on the eco-exergy theory, the spatial heterogeneity and distribution of tree layer and shrub layer of Pinus taiwanensis community in Daiyun Mountain were studied by geostatistics and GIS technology. The main results are as follows:(1) Tree layer and shrub layer are the main contributors to community ecology and structure, respectively. (2) P. taiwanensis population has higher competitiveness and survival probability in the community, and the contribution rate of community ecology is 98.39%, which plays a key role in maintaining the stability of community structure. (3) Eco-exergy and specific eco-exergy of tree and shrub layer have strong spatial autocorrelation on the local scale, and their spatial heterogeneity is mainly caused by structural factors, accounting for more than 75%. (4) The eco-exergy and specific eco-exergy of tree and shrub layer show obviously banded and patchy distribution. There are many obviously high value areas, the isoline is curved and dense, and the degree of spatial heterogeneity is high. The study could not only confirm the thermodynamic status of P. taiwanensis population in Daiyun Mountain, but also highlight its crucial role in maintaining community stability and complexity. The results could provide a theoretical basis for the succession dynamics and sustainable management of P. taiwanensis community.