In this study, we report the influences of distilled water and ammonium fluoride (NH4F) on morphology of pores in honeycomb-like titanium dioxide (TiO2) nanotube arrays. We observed the structure and arrangement of pores in the TiO2 nanotube arrays based on scanning electron microscopy images and analyzed the spatial distribution of the pores using fast Fourier transform and Voronoi diagram. We studied the individual pore properties including pore diameter, wall thickness, and interpore distance and found that locally connected ordering defects decreased with increasing distilled water concentration. Furthermore, we found that the optimum conditions of well-ordered hexagonal pore arrangement were 2 and 10 vol% distilled water with 0.2 and 0.4 wt% NH4F, respectively. Throughout this study, we provide a better understanding about the roles of distilled water and NH4F in forming well-ordered nanoscale pore structure with less ordering defects in the honeycomb-like TiO2 nanotube arrays.