The effect of intermittent aeration and an influent distributary on NH4+-N removal, total nitrogen (TN) removal, nitrous oxide (N2O) emission and the abundances of nitrogen removal and N2O emission functional genes in four types of ecological soil wastewater infiltration systems (ESWISs) (which were conventional ESWIS 1 (operated without aeration and influent distributary), ESWIS 2 (operated with intermittent aeration), ESWIS 3 (operated with influent distributary) and ESWIS 4 (operated with intermittent aeration and influent distributary)) were studied. Intermittent aeration in ESWIS 2 and 4 created aerobic conditions above 50 cm depth of the matrix and anoxic or anaerobic conditions in the lower matrix (below 80 cm depth). ESWIS 4 improved NH4+-N (to 90.1%) and TN (to 87.8%) removal efficiencies and increased the abundances of eight nitrogen removal and N2O emission functional genes (amoA, nxrA, narG, napA, nirS, nirK, qnorB and nosZ) in contrast with other ESWISs. The combination of intermittent aeration and influent distributary achieved the lowest N2O emission rate of 34.7 mg/(m2 d) in ESWIS 4. Intermittent aeration combined with influent distributary was recommended for ESWISs to enhance nitrogen removal and reduce N2O emission.