Redox-active organic materials, especially small molecules, are expected as alternatives to inorganic materials in electrochemical energy storage due to their multisite and highcapacity merits. Inspired by this, herein, we propose an organic small molecular material 1,4,5,8-naphthalenediimide (NDI) with multiple ion insertion sites as an efficient electrode material for seawater desalination. By providing a conductive and confined environment through a double-layer gel encapsulation strategy, we have solved the problem of dissolution and detachment of small molecular materials. Benefitting from multiple sites provided by carbonyl oxygen and the (−1−12) crystal plane, the fabricated composite electrode exhibits remarkable removal capacity for Na + (145 mg g −1 ) in 0.5 M NaCl solution. Furthermore, in natural seawater, the composite electrode demonstrates high stability and achieves impressive removal capacities for Na + (107 mg g −1 ), Mg 2+ (48 mg g −1 ), Ca 2+ (12 mg g −1 ), and K + (9.2 mg g −1 ), respectively. This work has realized the application of multisite small-molecule materials in seawater desalination by solving the problems of dissolution and detachment of organic small molecules, paving the way for developing novel efficient organic materials in electrochemical seawater desalination.