At the current stage, the traditional economic development model "Resource-Product-Waste Emission" of main industries in the Pearl River Delta Region has resulted great damage to the region's resources and environment. Environment pollution has been the key issue related to the enterprises' sustainable development. While different regions differ in industry types, industry structure and organization form. In this situation, it is imperative to introduce the concept of green technology innovation, and promote the manufacturing enterprises of the region conducting green technology innovation aiming at energy conservation, consume reduction and reduce pollution. Based on the current development of the manufacturing sector in Pearl River Delta region, this paper discusses challenges they face and their own advantages from the perspective of green technology innovation, and proposes policy recommendations accordingly. This paper argues that, in the background of green technology innovation, manufacturing development in the Pearl River Delta region faces some problems. The governments and the enterprises should unite and full play the Pearl River Delta region's advantage, and solve these problems from the followings: firstly, strengthen environmental monitoring and improve the enterprises' environmental protection work, and encourage enterprises to develop green technology and implement green innovation technology; secondly, extricate from the extensive growth, promote the intensive land use and realize the maximization of land use efficiency; thirdly, speed up industrial upgrading,and develop advanced manufacturing. Establishing the green innovation system of interaction consisting of enterprises, research-oriented universities, research institutes, governments and Technical institutions, so as to provide technical expertise for the development of the manufacturing in the Pearl River Delta region and develop green innovation manufacturing; fourthly, encourage enterprises' innovation and optimize the high-tech industries. Further increase the input in science and technology, promote the shift of innovation pattern, create a favorable industrial environment for business innovation and high-tech enterprises development, and enhance the ability of endogenous development. <<