The invention discloses a method for forming bi-active region shallow trenches. The method includes the steps of forming an etching barrier layer on a semiconductor substrate, exposing and developing first and second shallow trench areas where trenches of different depths are etched through a first photomask to complete etching of a barrier layer in an exposed area, exposing and developing the first shallow trench area where a trench with greater depth is etched by using a second photomask, completing etching an intermediate depth in the first shallow trench area, removing the second photomask, and integrally etching the first and second shallow trench areas to form the first and second shallow trenches with different depths. Through the design of the photomasks, low cost application of photomasks and optimization of etching process are achieved.