As the foundational carrier of socio-economic development and ecological security, territorial space reflects the degree of coordination between functional structure and efficiency output. However, most existing evaluation methods overlook the heterogeneous functional endowments of spatial units and therefore cannot reasonably assess the efficiency that each unit should achieve under comparable conditions. To address this limitation, this study proposes a function-oriented and interpretable framework for territorial spatial efficiency evaluation based on the Production–Living–Ecological (PLE) paradigm. An entropy-weighted indicator system is constructed to measure production, living, and ecological efficiency, and an XGBoost–SHAP model is developed to infer the nonlinear mapping between functional attributes and efficiency performance and to estimate the ideal efficiency of each spatial unit under Quanzhou’s prevailing macro-environment. By comparing ideal and observed efficiency, functional–efficiency deviations are identified and spatially diagnosed. The results show that territorial efficiency exhibits strong spatial heterogeneity: production and living efficiency concentrate in the southeastern coastal belt, whereas ecological efficiency dominates in the northwestern mountainous region. The mechanisms differ substantially across dimensions. Production efficiency is primarily driven by neighborhood living and productive conditions; living efficiency is dominated by structural inheritance and strengthened by service-related spillovers; and ecological efficiency depends overwhelmingly on local ecological endowments with additional neighborhood synergy. Approximately 45% of spatial units achieve functional–efficiency alignment, while peri-urban transition zones and hilly areas present significant negative deviations. This study advances territorial efficiency research by linking functional structure to efficiency generation through explainable machine learning, providing an interpretable analytical tool and actionable guidance for place-based spatial optimization and high-quality territorial governance.