Based on the first-tier disciplines evaluation ranking in 2012 by the Center of China Academic Degrees and Graduate Education under the Ministry of Education，this study analyzed the distribution features of the top 3 programs in each discipline and the universities they are located. The findings pointed out that although industry-based universities have shown substantial comprehensive strength and distinctive disciplinary features，they face the dilemma of “caught in the middle”. To improve the development of industry-based universities，this study calls for innovative ideas，deeper understanding，and general consensus. In terms of action to be taken，the Featured Discipline Projects need to be initiated in order to elevate the level of comprehensive strength of these universities；they also need to improve their governance structure，form modernized internal systems，strive to build more top-tier programs，and continue to boost their core competitiveness.