We investigated the effects of wood kraft pulp (WP) supplementation on ruminal pH, fermentation, and epithelial transcriptomic dynamics in Holstein cattle during the high-grain diet challenge. Five rumen-fistulated Holstein bulls (215.2 ± 20.4 kg of body weight; 7.4 ± 0.3 months of age) were used in a cross-over design without a wash-out period. After two weeks of adaptation period (100% forage feeding ad libitum), cattle were fed a high-grain diet containing corn flakes (control diet) or the WP as a half replacement of corn flakes in the control diet (WP diet) during the first 14 days, and then, the diets were switched for last 14 days. Ruminal pH was measured continuously, and the rumen fluid and epithelium (RE) were collected on the last days of each feeding period simultaneously with blood samples. mRNA expression profiles of the RE were examined by one-color microarray. The differentially expressed genes (DEGs) were investigated using the Ingenuity Pathway Analysis (IPA). The 24 h mean ruminal pH was not different between the control (n = 5) and WP (n = 5) groups (6.39 vs. 6.46, respectively), being higher in the WP group. The proportion of acetic acid tended to be higher in the WP group, and blood urea nitrogen concentration was significantly higher in the WP group compared with the control group. The top differentially expressed candidate genes were involved in inhibition of the immune and inflammatory responses by suppressing the expressions of M-SAA3.2 and IL-36 cytokine signaling pathway (IL36G, IL36A, and IL36RN) in the WP group. In silico analysis revealed that “Remodeling of Epithelial Adherens Junctions” was the most significant signaling pathway, and epidermal growth factor receptor was the most significant upstream regulators, which were involved in the adaptation of the RE to high-grain diet challenge. Furthermore, upstream regulator analysis suggested that microRNAs may be involved in a central role in the RE cellular regulations. These results suggested that WP supplementation as 50% replacement of corn flakes in a high-grain diet did not cause significant contrast in the rumen fermentation and blood metabolite profiles, preferably leading the activation of rumen epithelial transcriptomes to facilitate the development or adaptation of the RE in Holstein cattle during the high-grain diet challenge.