The invention discloses an ecological treatment system and method of a natural water body. The system comprises water purification treatment, aeration for oxygen enrichment and water body circulation;water purification treatment means that a treated water body is lifted to a water body reaeration purification device for purification, pollutants are cleared, and the water body transparency is improved; aeration for oxygen enrichment means that the purified water body is supplemented with dissolved oxygen to improve a redox potential of the water body; water body circulation means that water subjected to treatment of aeration for oxygen enrichment is returned to a renovated water body through a water body circulation oxygen enrichment device; then the water body circulation oxygen enrichment device is used for further supplementing the renovated water body with dissolved oxygen, promoting running water, further purifying the water quality, reducing ammonia nitrogen and improving the transparency and the redox potential. According to the ecological treatment system and method of the natural water body, water quality improvement, ecological remediation and landscape ascension are combined, the system and the method have the characteristics that energy is saved, the algal inhibition effect is good, ecological restoration is fast, the treatment cost is low, and the like, and the system and the method have better social benefits and ecological benefits.