The catfish, Pterygoplichthys pardalis, which belongs to the Loricariidae family, an invasive species which has caused huge damage to the ecological environment. However, the high-quality reference genome for the catfish has not yet been reported. In this study, we successfully assembled the first chromosome-level high-quality genome of P. pardalis using the data we produced from multiple sequencing platforms, which contains 26 chromosomes and with a scaffold N50 of 49.47 Mb. Different evaluation methods all indicate the high connectivity and accuracy of the P. pardalis genome we got. We predicated 23,859 protein-coding genes in the P. pardalis genome, and 22,169 (~92.92%) coding genes could be functionally annotated in public databases. Phylogenetic relationship analysis found P. pardalis was clustered with all the catfishes we used and diverged with them 132.5 million years ago. Besides, whole-genome collinearity analysis found that chromosome 6 of P. pardalis was aligned to two distinct chromosomes both for Ameiurus melas, Pangasianodon hypophthalmus and Ictalurus punctatus, indicating that there may have been a chromosomal fusion/fission event occurred. Furthermore, many immune-system-related genes were large-scale expanded in P. pardalis genome, which may make great contributions to their adaptive traits, even for the highly polluted environmental conditions, and successful invasion. Taken together, this study not only provides insights into the genetic basis of the successful invasion of P. pardalis, but also provides important data resources for comparative genomic analysis of P. pardalis in Siluriformes in the future.