This study explored the application of shale ceramsite (SC) overlaid onto active alumina (AA) to function as a double-layer substrate in tidal flow constructed wetland (TFCW, SC-AA-TFCW) for decentralized domestic sewage treatment. This was compared to AA or SC substrate alone (AA-TFCW or SC-TFCW) for nitrogen removal, variation of dissolved oxygen and porosity in TFCWs, as well as structure of bacterial communities at varied hydraulic load (HL) of 0.204–2.448 m3/m2 d with time ratio of the wet and dry phase of 3:1. The results demonstrate that SC-AA-TFCW removed 86% NH4+-N and 79% total nitrogen at HL of 0.612 m3/m2 d, which was better than AA-TFCW(76%) or SC-TFCW(49%). The higher nitrogen removal performance in SC-AA-TFCW was mainly attributed to enhanced oxygen transportation due to non-uniform flow field and irregular gap distribution in layered structure, as well as less pore blockage during long-term operation. Denitrifying bacteria including Dechloromonas, Acidovorax, Chryseobacterium and Thermomonas species took up 32% of the microbiome in SC-AA-TFCW, which was higher than in AA-TFCW (17%) and SC-TFCW (7.7%). This study highlighted the importance of layered structures and determined an optimal HL of TFCW to achieve an efficient and stable nitrogen removal for domestic sewage treatment.