In recent years, stricter environmental regulations coupled with increasing awareness of environmental protection have urged manufacturing companies to raise serious concerns on sustainable issues, such as removal of waste or toxic materials, enhancing energy saving, reducing water consumption and fossil carbon emissions, and reusing recyclable components. In practice, however, most green or sustainable projects for improving product design or process layout incur significant implementation costs during the inception. In order to balance the trade-offs between maximal present worth and limited financial resources, this study proposes a novel framework to assists a TFT-LCD panel company in implementing lean manufacturing systems and green production processes. Initially, the importance degrees of green requirements (GRs) are derived through analytical hierarchy process (AHP). Thereafter, by considering the dependences between GRs and GAs, grey relational analysis (GRA) is conducted to derive the priorities of green alternatives (GAs). Finally, binary integer programming (BIP) is used to determine the optimal project portfolios. More importantly, this paper concurrently takes lean manufacturing (removing waste of materials) and sustainable process (reducing energy consumption) into account.