Hierarchical SnO nanocrystals are synthesized by a reproducible and facile way via decomposition of an intermediate product tin oxide hydroxide, Sn6O4(OH)4. By changing the amount of injecting water, layerplate-like, nest-like, stepwise-bipyramid-like, and defective stepwise-bipyramid-like hierarchical SnO nanocrystals could be obtained. All of these hierarchical SnO nanostructures are constructed by smaller nanosheets. The driving force of aggregation is reducing the surface energy of nanocrystals. Water played a key role in the control morphologies of hierarchical SnO nanostructures. The water control decomposition (WCD) mechanism was proposed to explain the effect of water on the morphologies. On the basis of reaction kinetics, the different superfluous injected water after reaction would restrain the decomposition of Sn6O4(OH)4 to SnO nanosheets; a different amount of superfluous injected water would induce a different reaction rate. At different reaction rates, SnO nanosheets would have different sizes and different approaches to aggregation, and different hierarchical SnO nanocrystals appeared by injecting different amounts of water into the reaction. Typically, hierarchical SnO nanocrystals as an anode material for lithium ion batteries are studied. These SnO nanocrystals show good potential for lithium battery materials. Among these SnO nanostructures, the stepwise-bipyramid-like nanostructure shows the best properties.