Decreasing groundwater temperature by freshwater extraction and cold-water recharge can mitigate seawater intrusion in coastal aquifers. However, the impact of frequently employed and easily executed intermittent well operations on this has been overlooked. This study numerically examines temperature and salinity distributions in coastal aquifers subject to intermittent freshwater extraction and cold-water recharge (IER) at an equal rate. Results show that IER maintains an equivalent effect on inhibiting seawater intrusion as the continuous method, while IER during cold seasons reduces operational time and cooling heat consumption. For instance, numerical test on a realistic aquifer shows that 90 d of IER could lead to a 75% decrease in operational time and a 29% reduction in cooling energy usage compared to the continuous method. The mitigation effectiveness depends on the averaged seaward hydraulic gradient, which is affected by heat storage reduction above the saltwater wedge. The cold-water plume from IER is convergently transported and discharged, creating a pronounced fluctuation of heat storage reduction and thereby resulting in a delayed periodic variation of the hydraulic gradient. As salt efflux is an integrated result of periodically changing hydraulic gradients, total salt mass exhibits a delayed and prolonged response to the variation of heat storage reduction. Sensitivity analyses show that a far recharge distance and reduced aquifer permeability increase the delay between heat storage reduction and total salt mass, and low recharge temperature facilitates seawater intrusion mitigation. This study demonstrates the importance of the intermittent method in inhibiting seawater intrusion and has implications for sustainable management of coastal groundwater resources.