Ammonium paratungstate (APT) is an important intermediate for the production of tungsten-containing products. However, its morphology problems caused by crystal agglomeration affect its properties. In this paper, the mechanism of agglomeration during the evaporative crystallization of APT was studied. The experimental result reveals that the temperature, as a critical parameter, significantly affects hydrates purification of crystallization. Combined with on-line and off-line analysis, it is proposed that the crystal agglomeration mainly results from hydrate transformation from heptahydrate to pentahydrate. Furthermore, based on this agglomeration mechanism, the strategy of adding seeds was applied to control the supersaturation within the metastable region and to avoid the nucleation of heptahydrates. The effect of seeds properties, such as the effect of its mass and size on the particle size distribution and agglomeration degree of the products, were investigated in batch crystallization. Finally, we obtained monodisperse crystals of pure APT·5H2O with better performance.