Being a top bio-derived value added chemical, malic acid is used widely in various industries including chemical engineering, food, and pharmaceutical. It is of great significance to produce malic acid by converting sustainable cellulosic raw materials. This review has introduced and summarized the malic acid bio-refinery process, which was inoculating the fermented raw materials, analyzing the main metabolic pathways of the fermented raw materials, identifying the key enzymes for malic acid production, and determining the malic acid metabolism improvement strategy. At the same time as the technical summary, the correlation between the internal metabolism of the transformed organism and the external conditions was analyzed, and the forward trend of malic acid biotransformation was proposed. The forward trend was simultaneous of saccharification and fermentation processes to improve transformation efficiency, improving and enhancing cell tolerances and fermentation adaptabilities, promoting co-fermentation of five-carbon sugars and six-carbon sugars, decreasing greenhouse effect and controlling energy balance. This review was expected to provide meaningful insight to the development of the malic acid bio-refinery industry.