Microbial systems play a crucial role in the synthesis of the chiral drugs and drug intermediates, contributing significantly to the pharmaceutical industry. Chirality refers to the existence of two non-superimposable mirror-image molecules (enantiomers), which can have vastly different biological activities. In many cases, one enantiomer may be therapeutically active, while the other could be ineffective or even harmful. Thus, the ability to produce chiral compounds with high specificity is essential in modern medicine. Functional microorganisms and enzyme (derived biocatalysts) have great potential in the biotransformation of synthetic chemicals in drugs with high enantiomeric, chemical and regional selectivity. The Chiral feature is an important factor in the efficacy and safety of many therapeutic drugs. Biocatalysis is becoming a major sub-component in the toolbox of medicinal chemistry. In fact, many intermediates of important therapeutic agents have been successfully synthesized by biocatalysis. Currently, about 57% of drugs on the market are chiral drugs, and about 99% of pure natural products are chiral compounds. Here, we have summarized various biocatalytic systems capable of synthesizing chiral drugs and intermediates and discussed their potential applications in the pharmaceutical industry. With the emphasis on green chemistry, the further development and use of biocatalysis in drug production is expected to increase.