Microscopic plastic particles (0.1 µm–5 mm) are widespread hazardous pollutants, and microfibres (MFs) are their dominant shape in habitats. Previous field and laboratory studies have demonstrated that MFs enter the coelomic fluid of sea cucumbers from the water through the respiratory tree. However, the possible mechanism underlying the toxicity of this process is not well understood. Herein, RNA-Seq was used to examine the responses of the respiratory tree during the MF transfer process in the sea cucumber Apostichopus japonicus. Polyester synthetic MFs were used, and the number of transferred MFs was controlled to the amount reported from the field. The results showed that the MFs altered gene expression as the transfer process increased. The top genes regulated by MF transfer were mainly related to metabolic processes and signal transduction pathways, with upregulated genes following low MF transfer and downregulated genes following high MF transfer. Functional enrichment analysis revealed the pathways in which differentially expressed genes were enriched under different MF transfer scenarios. The transcriptomic findings were further supported by histological observations, which revealed injury and loss of cell components. This study contributes to understanding the effects of MFs in a valuable echinoderm species through transcriptomic and histological examinations.