Taiwan and mainland China have gradually formed an industrial cooperation relationship with Taiwan-funded enterprises（Taiwanese entrepreneurs）as a link. Overall，the scale of projects invested by Taiwanese entrepreneurs in the mainland is generally small，and the small and medium-sized enterprises are the main body. According to a brief analysis of the main Taiwan-funded industries，including information and electronic，semiconductor，petrochemical，and machinery，it can be found that in the current cross-strait industrial cooperation，the vertical division of labor of Taiwanese entrepreneurs between Taiwan and mainland is the mainstream，and the spillover effect of Taiwanese entrepreneurs in mainland is limited. Taiwan’s industrial layout in mainland is concentrated in manufacturing sectors，with the rise of the importance of the mainland domestic demand market，the cross-strait cooperation in technology research needs to be improved. With the rapid growth of the mainland economy，the previous structure of cross-strait industrial cooperation that Taiwan provides technology and capital，and mainland provides raw materials，semi-finished products and labor has changed. The complementarity of elements between Taiwan and mainland is reduced，and their competition is increasing. The operating costs of Taiwan-funded enterprises in mainland China have risen，and the previous foundry business model of Taiwanese companies is difficult to sustain. All of these are the challenges of Taiwanese investment in the mainland China in the current cross-strait relations.