Separating apparatus and method thereof of biosubstance

A separating apparatus and a method thereof of biosubstance are provided. The separating method includes the following steps: providing a control module to select and perform a positive separation process or a negative separation process according to the type of a target biosubstance; providing a pipette pump to inject a first magnetic bead reagent or a second magnetic bead to a specimen according to the selected separation process, and the first immunomagnetic beads in the first magnetic bead reagent or the second immunomagnetic beads in the second magnetic bead reagent are combined with the target biological substance, wherein, when the forward separation process is selected, the pipette pump is used to add the first magnetic bead reagent to the specimen, and when the negative separation process is selected, the pipette pump is used to add the second magnetic bead reagent to the specimen; providing a magnetic separation rack to generate a magnetic field to enrich the target biological substances, so as to s