The invention discloses an underflow constructed wetland ecological system for disposing rural domestic waste and a disposing method. By adding root advantageous microorganisms in a canna water planting system, ratio of Alkaligenes, flavobacterium, lysobacter, Pseudomonas and other advantageous germs can be rapidly increased, the abundance of dioxygenase, dehydrogenase, phosphate dehydrogenase, urease, nitrate reductase, and dehydrogenase gene in catalase gene in the constructed wetland can be improved; two kinds of wetland plants can be planted in an intersecting manner, thus the different plant root secreta can be generated and a rich root microbial community structure is formed; the underflow constructed wetland ecological system can remove COD, ammonia nitrogen and total phosphorus atthe same time. Then the method of alternatively running continuous water feeding-intermittent water feeding is applied, thus the nitrogen removal efficiency is promoted while the system is stably operated. The method fully applies the advantages of the constructed wetland, strengthens the rapid construction of the constructed wetland ecological system, and optimizes the wetland running mode; the underflow constructed wetland ecological system is significant in environment, economic and social values.