The invention discloses a system and a method for treatment of shallow groundwater pollution. The system comprises a seepage reservoir which is built at a site in a groundwater contaminated area, anda water pump which is arranged at the bottom of the seepage reservoir and used for pumping treated groundwater out of the seepage reservoir, wherein the bottom of the seepage reservoir and the slope surrounding the seepage reservoir are respectively covered with a filling medium layer which is composed of a limestone gravel layer with a thickness of 15 to 50 cm, an active carbon layer with a thickness of 15 to 50 cm, a zeolite layer with a thickness of 15 to 50 cm and a synthetic ion-exchange resin layer from top to bottom. The construction method comprises the following steps: site selection,seepage reservoir digging, treatment of the slope and a base, medium filling, sediment removal, and underground recharging. The invention has the following advantages: construction is simple; technical difficulty is low; the treatment range of groundwater is broad; the treated groundwater is pumped back to underground, so sustainable circulating utilization of groundwater resources in arid and semi-arid areas can be maintained; and characteristics of high efficiency and economy for treatment of shallow groundwater pollution are achieved.