The invention discloses an internal cooling structure for isolating a rotor in a magnetic suspension fan. The internal cooling structure includes an enclosure, a magnetic suspension bearing, a rotor, a stator and an impeller, the magnetic suspension bearing and the stator are supported in the enclosure, the rotor is rotatably arranged in the magnetic suspension bearing and the stator, one end of the rotor stretches out of the enclosure and is fixedly connected with the impeller, the internal cooling structure also includes a hood and a barrel-shaped sheath with one open end and one closed end, the sheath is sleeved between the rotor and the magnetic suspension bearing and between the rotor and the stator, the open end of the sheath stretches out of the enclosure, the hood is fixedly connected with the impeller, a through hole is arranged in a shaft center direction of the rotor, the through hole is communicated with an inner cavity of the sheath, and an exhaust hole communicated with the through hole is arranged on the hood. The rotor is internally provided with a through hole, so that high-pressure gas in the sheath can be led to an impeller front end low-pressure area and discharged through the exhaust hole.