The invention discloses a system and a method for treating slightly alkaline secondary effluent through magnetic ion exchange resin coupled catalytic ozonation circulating reflux, and the system comprises a high-density resin mixing tank, a resin sedimentation tank and a catalytic ozonation tank, wherein the high-density resin mixing tank is provided with a water inlet, a regenerated resin inlet, a mechanical stirrer, an oxidized effluent backflow water inlet, a regenerated or waste resin outlet, a resin backflow inlet and a resin sedimentation tank connector; the resin sedimentation tank is provided with a resin backflow outlet, a first inclined tube sedimentation plate and an overflow weir; the catalytic ozonation tank is provided with a resin-based catalyst, a baffle plate, an ozone generator, an aeration device, a water outlet, an oxidation reflux water outlet and a second inclined tube precipitation plate. The magnetic resin technology and catalytic ozonation are organically combined from the perspective of system design and operation, the treatment efficiency is improved, the service life of the resin is prolonged, the cost is saved, the waste magnetic resin is recycled, and the water treatment amount is increased.