Microalgae are the third generation of biomasses that have received lots of attention due to their high energy content and ability to capture carbon dioxide from the air. However, there are some techno-economic challenges for their world commercialization. A variety of fuels can be extracted from microalgae, and in addition to these fuels, algae by-products can be used to commercialize this industry. Various processes will be performed on microalgae to finally desired products can be extracted. In this research, an integrated system has been designed for the simultaneous production of ethanol, methane, and hydrogen from Chlorella vulgaris microalgae. The re-sults showed that after culturing, harvesting, and increasing the concentration of the solution in addition to the main products such as ethanol, methane, and hydrogen, by-products including acetic acid, methyl acetate, ethyl acetate, furfural and etc. can be utilized for commercializing microalgae industry. Also, another purpose of this study is to apply Pinch Analysis to the mentioned system, which will ultimately improve the concentration of microalgae in the photobioreactor. The results of Pinch Analysis show that by increasing the concentrations of microalgae, carbon dioxide, and nutrients in the photobioreactor inlet up to 2.35 gr/l, the desired amount of demands can be met by the new supplies.