The invention relates to a farmland nitrogen and phosphorous non-point source pollution control and recycle system, and a method thereof. The system comprises a water collector, an adsorption unit and a water store which are sequentially arranged from the upstream to the downstream according to farmland surface runoff and underground runoff paths. The water collector, the adsorption unit and the water store are sequentially transversely arranged according to the farmland surface runoff and underground runoff paths, so when rain falls or irrigation is carried out, the farmland water is surplus, meets in the water collector through the farmland surface runoff and underground runoff, the water in the collector continuously downward flows and goes through the adsorption unit, nitrogen (N) and phosphorous (P) are adsorbed, the purified farmland drainage enters the water store, and the superfluous purified drainage is discharged to a river and a lake; and when farmland recharging is carried out, the water which reversely flows goes through the adsorption unit for the N and P desorption, and the desorbed N and P enter the water collector with the water flow, afresh enter the farmland and are adsorbed and utilized by crops. Compared with the prior art, the method has the advantages of pollution control, recycle, fertilizing cost saving and the like.