Panonychus citri is a significant pest of Rutaceae plants. Chitin deacetylase is a key gene in chitin metabolism and the insect molting process. In this study, The PcCDA1 and PcCDA2 genes of P. citri were cloned and identified. The expression of PcCDA1 was higher during the egg stage, while PcCDA2 exhibited the highest expression during the larval stage, with their expression levels showing a clear periodicity. Using RNAi technology to silence the expression of the PcCDA1 and PcCDA2 genes in the mite, the results indicated that only 20.85% successfully molted, while the deformity rates were 78.81% and 85.44%, respectively. HE staining and microscopic observation revealed that silencing PcCDA1 and PcCDA2 caused an increase in the epidermal thickness of P. citri by 1.87 μm and 5.706 μm, respectively. Additionally, silencing PcCDA also significantly reduced the relative mRNA expression levels of chitin synthesis genes (PcCHS1 and PcCHS2) and degradation genes (PcCHT1, PcCHT2, and PcCHT4). These results suggest that the PcCDA gene is crucial for normal molting and epidermal development, providing new scientific evidence for molecular target-based green pest control strategies.