Covalent organic frameworks (COFs) have emerged as an excellent support for heterogeneous catalysis due to their regular pore structure and high specific surface area. Herein, a series of porous TpPa-1 with different morphologies and structures were achieved by adjusting the ratio of water to acetic acid in the solvent-thermal process, and Pd@TpPa-1 catalysts were obtained with Pd solution impregnation. Notably, Pd@TpPa-1-100 prepared with 100 wt % water as the catalyst has superior catalytic properties in the phenol hydrogenation to cyclohexanone, and its turnover frequency (TOF) of 33.1 h(-1) is about 7 times higher than that of Pd@TpPa-1-0 synthesized with 100 wt % acetic acid as the catalyst. The two-dimensional (2D) nanosheet structures, highly dispersed Pd nanoparticles (NPs) with small particle size, and superhydrophilicity should be responsible for the superior catalytic performance of Pd@TpPa-1-100. Furthermore, Pd@TpPa-1-100 also has better catalytic performance in the hydrogenation of catechol, resorcinol, and hydroquinone than Pd@TpPa-1-0 and exhibits superior catalytic stability. This study provides a new approach for the structural regulation of metal-based COF catalysts.