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Clubroot is an infectious root disease caused by <i>Plasmodiophora brassicae</i> in <i>Brassica</i> crops, which can cause immeasurable losses. We analyzed integrative transcriptome, small RNAs, degradome, and phytohormone comprehensively to explore the infection mechanism of <i>P. brassicae.</i> In this study, root samples of <i>Brassica rapa</i> resistant line material BrT24 (R-line) and susceptible line material Y510-9 (S-line) were collected at four different time points for cytological, transcriptome, miRNA, and degradome analyses. We found the critical period of disease resistance and infection were at 0–3 DAI (days after inoculation) and 9–20 DAI, respectively. Based on our finding, we further analyzed the data of 9 DAI vs. 20 DAI of S-line and predicted the key genes <i>ARF8</i>, <i>NAC1</i>, <i>NAC4</i>, <i>TCP10</i>, <i>SPL14</i>, <i>REV,</i> and <i>AtHB</i>, which were related to clubroot disease development and regulating disease resistance mechanisms. These genes are mainly related to auxin, cytokinin, jasmonic acid, and ethylene cycles. We proposed a regulatory model of plant hormones under the mRNA–miRNA regulation in the critical period of <i>P. brassicae</i> infection by using the present data of the integrative transcriptome, small RNAs, degradome, and phytohormone with our previously published results. Our integrative analysis provided new insights into the regulation relationship of miRNAs and plant hormones during the process of disease infection with <i>P. brassicae.</i>