NH4Cl is one of the nitrogen sources for microalgal cultivation. However, excessive amounts of NH4Cl affects microalgal physiology and biomass contents. In this study, the effects of ammonium on microalgal growth and TAG content in the green microalga (Chlamydomonas reinhardtii) was investigated. Microalgal growth and TAG content under photoautotrophic conditions were found to be unchanged with 17 mM of ammonium, while this compound interfered with microalgal growth and induced TAG content under mixotrophic conditions with acetate supplementation. This suggested that ammonium could induce TAG production when acetate occurred in microalgal cultivation. Further, the effects of two different concentrations of NH4Cl (17 mM and 60 mM) on the cells under mixotrophic conditions were investigated. The results showed that both concentrations reduced microalgal growth, but induced total lipid and TAG content, especially after a 4-day cultivation. The oxygen evolution and Fv/Fm ratio showed that both concentrations completely inhibited the oxygen evolution on Day 4. The 60 mM NH4Cl reduced the Fv/Fm ratio from 0.7 to 0.48 indicating that ammonium supplementation directly affects the microalgae photosynthesis performance. A total of 1782 proteins were successfully identified using proteomics analysis. Among them, there were nine overexpressed proteins and four proteins were underexpressed. Using the protein–ligand interaction analysis, nitrogen metabolism is involved under NH4Cl conditions. This information can provide biochemical knowledge for microalgae development for sustainable energy usage.