Hierarchical MoS2 thin films nanostructured with orthogonally oriented vertically and horizontally aligned layers were designed and excellent passive Q-switching behavior in a fiber laser was demonstrated. A special solvothermal system containing a small amount of water was applied to synthesize such hierarchical MoS2 nanofilms, in which the reaction rate is carefully controlled by the diffusion rate of the sulfur precursor. Wafer-scale MoS2 thin films with hierarchical structures are formed on various substrates. Moreover, the hierarchical MoS2 thin films consisting of both vertical and horizontal layers can be tuned to possess only horizontally aligned layers by controlling the solvothermal time. To show the potential application proof-of-concept, the nonlinear optical performance of the hierarchical MoS2 was investigated. Superior passive Q-switching behavior in a fiber laser with a minimum pulse width of 2.2 μs was observed.