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The National Ecological Barrier Zones are an important part of China’s ecological security strategy. The construction of a scientific and reasonable ecological security pattern (ESP) is important for the healthy development of national ecological barrier zones. The existing literature does not consider the impact of the potential changes in ecosystem health and land use on ESP construction. In this study, we considered a typical composite national ecological barrier area, the Sichuan-Yunnan ecological barrier, to analyze the ecosystem health of such areas; we considered the probability of future land growth change, circuit theory, and ecosystem service trade-off and synergy, to construct a sustainable ESP. Spatial heterogeneity was observed in the ecosystem health level of the Sichuan-Yunnan ecological barrier; the high-value areas of ecosystem health were mostly distributed in the central and southern parts of the study area, but the low-value areas were mostly distributed in the northeastern and western regions. The ESP contained 246 ecological sources (distributed in the forest and grassland contiguous areas in the south, central, and northeast regions), 563 ecological corridors that portrayed obvious differences in spatial distribution, 123 ecological pinchpoints, 231 ecological barriers, and topographic gradient characteristics. Based on this data, we proposed the relevant policy opinions on zoning control. The results show that incorporating trade-offs for ecosystem services into ecosystem health assessments can lead to a more effective selection of ecological sources. Meanwhile, the ESP constructed by using the probability of land growth changes to correct the resistance surface can more truly reflect the need for ESP construction under the future development trend. The research framework of “ecosystem health assessment that incorporates ecosystem service trade-offs - the probability of future land growth changes - circuit theory” could address the technical issues in constructing the ESP of compound large regional/national ecological barrier regions and key ecological function areas.