Enterprise is the cell of market economy，the carrier of industry and the taxpayer itself. Nurturing enterprises is a process of cultivating tax source. Industrial incubation base can efficiently nurture enterprises and generate tax revenue. On the basis of expounding the relationship between the construction of industrial incubation base and the cultivation of tax source，this paper analyzed the current situation，characteristics and problems of the regional tax source structure in the Shenzhen-Shantou Special Cooperation Zone. The paper combined the real situation of economic development in the cooperation zone，applied the basic theory of economic taxation，and proposed suggestions for the construction of the industrial incubation base and the cultivation of tax source in the cooperation zone.