The invention discloses a system and method for treating rural sewage by using an ecological system based on multi-submerged plant combinations. From the water inlet to the water outlet, the system sequentially comprises three regions in a pond, wherein a submerged plant combination A, which comprises more than any two of hydrilla, waterweed, Najas minor, curly pondweed and bog pondweed, is planted in the first treatment region; a submerged plant combination B, which at least comprises Vallisneria spiralis and vallisneria spinulosa, is planted in the second treatment region; and a submerged plant combination C, which comprises more than any two of hydrilla, waterweed, Najas minor, Vallisneria spiralis, vallisneria spinulosa, curly pondweed, bog pondweed, watermilfoil and hornwort, is planted in the third treatment region. The system and method are simple to implement, have the advantages of low cost and favorable effect, and do not need additional pipe network engineering and land; and the effluent water can achieve Grade 1 A above in Discharge Standard of Pollutants for Municipal Wastewater Treatment Plant. The system can be used as a natural landscape, and has the advantages of high transparency of the water body, high biodiversity and high ecological landscape value.