The production of di-n-butyl-ether (DNBE), for use as a blending agent in diesel fuel, is very attractive because the reactant (n-butanol) can be readily produced by the fermentation of bio-derivatives. The dehydration of n-butanol is known to show diffusion-limited characteristics on porous catalysts, such as zeolites or mesoporous supported catalysts. In order to overcome this limitation, herein, we synthesized silica spheres (DSS) with three-dimensional (3D) open pores by a hydrothermal reaction for use as a catalyst for the dehydration of n-butanol. In addition, supported heteropolyacid (PW) catalysts were also prepared on various porous silicas, DSS, SBA-15 and microporous silica (mi-S), to investigate the effect of 3D pore structures on the conversion of n-butanol to DNBE against 2D mesoporous and microporous materials by quantitative calculation. PW/DSS showed the best performance among the catalysts at various temperatures (453, 473, and 493K). The extent of catalytic performance enhancement was quantified by calculating the effectiveness factor (η) based on kinetics data. The η values for PW/DSS, PW/SBA, and PW/mi-S were determined to be 0.83, 0.63 and 0.52, respectively.