Hierarchical porous materials especially the silica-based ones are undergoing rapid development due to potential applications in the fields of catalysis, adsorption, separation, and biomedical processes. Although various synthesis methods involving emulsions, colloids, and surfactants have been reported, synthesis of hierarchical porous silicas (HPS) with complex mesophase transformations by using a four-component microemulsion (surfactant/cosurfactant/oil/water) templating approach is still challenging. Herein, we have successfully synthesized porous silica materials by introducing n-butanol (Bu) as the cosurfactant and 1,3,5-trimethylbenzene (TMB) as the oil component in a four-component P123–n-butanol–1,3,5-trimethylbenzene–water system. By simply increasing the molar ratio of Bu to TMB continuously while keeping a fixed mass of TMB in the mean time, mesophase transformations, progressing from mesocellular foam (MCF) via a vesicle-like structure to an ordered 2D hexagonal structure (SBA-15), can be observed. Moreover, an opposite phase transformation process was also proved by gradually increasing the molar ratio of TMB to Bu by maintaining a certain value for the Bu content in the initial system. All the mixed phase silica materials including hexagonal–vesicle, MCF–vesicle–hexagonal, and MCF–disordered-SBA-15-type show hierarchically porous structures. The mechanism for the mesophase transformation was proposed and a micelle/microemulsion method with bimodal templates was put forward to form hierarchical porous silicas with a mixed phase of the MCF–disordered-SBA-15-type structure. Furthermore, a series of Al-containing mesoporous silicas with different structures (hexagonal, vesicle, MCF, MCF–vesicle–hexagonal, and MCF–disordered-SBA-15-type) were used as catalyst supports for dibenzothiophene hydrodesulfurization. The NiMo/Al-hierarchical porous silica catalyst with pore structures of MCF–disordered-SBA-15-type displayed the best hydrodesulfurization performance among all the studied catalysts.