With the aim of tailoring and controlling surface assembly, multifunctional flame retardants (FRs) were obtained based on depositing alginates and silane coupling agents on brucite via the spray-drying-assisted layer-by-layer assembly technique. The assembly was controllable in both structure and gradient mass. Two series of FRs were named CuFR1-3 and NiFR1-3 based on the assembly content of metal alginates. With the assistance of spray drying, good compatibility between FRs and ethylene-vinyl acetate (EVA) was obtained, resulting in better mechanical properties. Meanwhile, the FRs improved flame retardancy and smoke suppression when used in EVA composites. With 55 wt % loading, composites with CuFR3 and NiFR1 passed UL 94 V-0 rating, while those with brucite were not rated. The peak of heat release rate decreased by 51.7 and 49.3% while the residue increased by 9.8 and 11.9%, respectively. The FRs also reduced the smoke and CO production rates. For the two series of FRs, the relationship between FR efficiency and alginate contents is different. The CuFRs assembled more copper alginates and exerted better flame retardancy caused by lower catalytic graphitization. NiFRs exerted a higher catalyzing efficiency at low assembly content. However, at high assembly content, the catalytic graphitization effect would decrease by thermally oxidized degradation leading to excess nickel alginates.