Hydroxynitrile lyase (HNL) from cyanogenic millipede Oxidus gracillis (OgraHNL) has been discovered as a crucial enzyme involving in the cyanogenesis pathway. Here, the crystal structures of OgraHNL complexed with sulfate, benzaldehyde (BA), (R)‐Man, (R)‐2‐Cl‐Man, and acetone cyanohydrin (ACN) were solved at 1.6, 1.7, 2.3, 2.1, and 2.0 Å resolutions, respectively. The structure of OgraHNL revealed that it belongs to the lipocalin superfamily. Based on the structure, positive mutants have been designed to further improve the catalytic activity and enantioselectivity of the enzyme on asymmetric hydrocyanation and Henry reactions.