The food industry is not only an important livelihood industry but also an important index of national economic development. In Taiwan, food industrialists emphasize the domestic market. In addition, they have continuously established factories in Southeast Asia and mainland China to expand the scale. In order to face the pressure of the international competitiveness and the strike of the food security turmoil, Taiwan food companies should increase operating performance and enhance profitability. This study collected 15 listed ASEAN-concept food company operating data from 2011 to 2013. Number of employees, R&D expenses, and net value of fixed assets were regarded as the input variables. Operating revenue and after-tax net income were regarded as the output variables. Furthermore, this study used Data Envelopment Analysis (DEA) to measure operating performance of Taiwan‘s food industry, then offered appropriate recommendations. The Results showed that five companies got outstanding performance, including DaChan, Uni-President, Standard Foods, Lian Hwa, and Ten Ren. During 2011-2013, their overall efficiency was 1. These companies‘ return to scale was in a constant state. The inefficient factor of most DMUs was the scale of inefficiency. In these three years, DaChan got the best operating performance and the highest reference number of these five companies. Therefore, it became the benchmarking learning model of most inefficient companies. Slack Variable Analysis showed that too many employees and R&D expenses were the main reasons which caused the food companies‘ management inefficiency. Promoting after-tax net is also the key reason to enhance operating performance.