Improving resource efficiency and reducing waste discharge are the inevitable trend of the development of sustainable machining system. Therefore, a data-driven sustainability evaluation method of machining system is proposed. The input (energy, materials, equipment, R&D and services), and output (wastes and products) data of machining system are collected. These dimensional data are processed by emergy. The emergy flow calculation model of the machining process is established for data modeling, and the sustainability evaluation index of machining system is constructed for data analysis. Finally, an engine base machining process is taken as case study for innovative practice; and the targeted process optimization is adopted based on its sustainability evaluation for innovative practice. The feasibility and effectiveness of the method are verified. This study provides theoretical and methodological support for promoting the sustainability of the manufacturing industry.