The invention provides a hand-eye coordination control system and method of a split type minimally invasive surgery robot, belongs to the field of medical robot manipulation and aims to solve the problem that hand-eye coordination inconformity occurs frequently in the control process of an existing minimally invasive surgery robot. The hand-eye coordination control system comprises a main console, a first instrument holding arm, a second instrument holding arm, a mirror holding arm, a first surgical instrument, a peritoneoscope and a second surgical instrument. The main console is provided with a 3D display system, a 3D display, a first main operation hand, a second main operation hand, an industrial personal computer and an industrial router, and the peritoneoscope is mounted on the mirror holding end of the mirror holding arm.