The stable operation of subsurface flow (SSF) constructed wetlands (CWs) depends on the adopted maintenance and management strategies. To determine a suitable resting period for SSF CWs, this study investigated and compared the impacts of three resting periods on plant physiological metabolism, wetland purification effectiveness, and microbial responses. The results revealed that resting operations induced morphological adaptations in wetland plants, significantly enhanced the root-shoot ratio and specific root length. A 2-d resting period enhanced oxygen secretion from plant roots, which was beneficial for SSF CW reoxygenation, leading to significant increases in the average removal rates of chemical oxygen demand and total phosphorus. After the resting operation, the inorganic phosphorus solubilization and transporters function of rhizosphere microorganisms were enhanced, resulting in efficient phosphorus removal. The functional genes related to nitrification, nitrogen fixation, and assimilation were increased, and a 2-5 d resting period facilitated the aerobic nitrification in SSF CWs. Inversely, an excessively long resting (>5 d) significantly inhibits plant and microbial activity, resulting in a deteriorated pollutant removal performance. Plants regulate rhizosphere microorganisms by adjusting root traits, which are the key factors and important reference indicators guiding the formulation of the operation and maintenance strategies for SSF CWs during resting periods.