The mixed culture fermentation is an important environmental biotechnology that converts biodegradable organic wastes to valuable chemicals such as hydrogen, methane, acetate, ethanol, propionate, and so on. For the multistep process of hydrolysis, acidogenesis, acetogenesis/homoacetogensis, and methanogenesis, the typical metabolic reactions are firstly summarized. And then, since the final metabolites are always a mixture, the separation and purification processes are necessary to couple with anaerobic fermentation. Therefore, several typical coupling technologies including biogas upgrading, two-stage fermentation, gas stripping, membrane technology of pervaporation, membrane distillation, electrodialysis, bipolar membrane electrodialysis, and microbial fuel cells are summarized to separate the metabolites and recover energy. At last, the novel technologies such as the controlled metabolite production, medium chain carboxylic acid production, and high temperature ethanol recovery in thermophilic mixed culture fermentation are also reviewed. However, the novel concepts are still needed to meet the demands of better overall performances and lower total costs.