Based on the perspective of new structural economics, this paper makes an empirical analysis of China Industry Business Performance Data from 1998 to 2013, and explores the influence of government development strategy on enterprises’ employment. The results show that the development strategy deviating from local comparative advantages has a significant negative impact on the employment. The conclusion is robust under the settings of different core explanatory variables, a different sample size and an instrumental variable regression. And this negative impact is mainly aimed at non-state-owned enterprises and is more obvious in regions with a lower degree of marketization. For this reason, we should continue to give full play to the decisive role of the market in resource allocation, improve diversified evaluation mechanism for government performance, give better play to the role of the government in making the best use of the situation, and eventually promote the organic combination of effective market and competent government, so as to unleash the potential of enterprises in providing job opportunities.