Based on accounting or market performance evaluating of a set of peer entities called Data Envelopment Analysis (DEA) is relatively new “data oriented” approach. This study applying DEA approach aims to evaluate corporate performance differentials between family and non-family business of small and medium enterprises in Mongolia. The principle of those corporate governance structures is formulating connection between family owners and business leader along with to develop approach and mechanism regulation of family business. This research focuses on sixty family and non-family firms which is all small and medium enterprises from manufacturing industry in Mongolia. The empirical results may offer improvement practice for SME-family business in small developing countries. The main purpose of study comparison between standard measurement of profitability for hypothesis comparative efficient within an important difference between family and non-family businesses. All efficiency scores are higher in family business and family firms are more profitable. But the result also demonstrates that non-family business earns more profitability (return on assets) compare with family business.