The invention provides a selective brain-body temperature bidirectional regulation and control system for small animals, which is used for respectively regulate and control the temperatures of the brain and the body of a small animal. The selective brain-body temperature bidirectional regulation and control system comprises a body temperature regulation and control subsystem and a brain temperature regulation and control subsystem, wherein the body temperature regulation and control subsystem comprises a body supporting panel, four pillars, a first countercurrent exchange device, a dual-temperature independent-control temperature controller, two thermocouple temperature sensitive probes and a computer; the brain temperature regulation and control subsystem comprises a brain supporting panel, a second countercurrent exchange device, a drainage device, a water collection device, two connecting guide pipes, a normally-open solenoid valve, an intelligent temperature controller and a thermocouple temperature sensitive probe. The selective brain-body temperature bidirectional regulation and control system can realize differential temperature regulation and control, as well as bidirectional temperature regulation and control, of the brain and the body of the small animal, can quickly regulate and control to obtain the target temperature within 5-10 min, and can also achieve accurate temperature regulation and control within a target temperature permitted range.