There are provided a method of manufacturing a three-dimensional structure, and three-dimension formation composition, by each which a three-dimensional structure can be manufactured with high dimensional accuracy, and provided a three-dimensional structure manufactured with high dimensional accuracy.There is provided a method of manufacturing a three-dimensional structure, in which the three-dimensional structure is manufactured by laminating a layer, the method including: forming the layer using a three-dimension formation composition containing particles, a binding resin, and a water-based solvent; removing the water-based solvent from the layer by heating the layer; and applying a binding solution containing a binder to the layer, in which the binding resin has an ammonium salt of a carboxyl group as a functional group.