The disease caused by scuticociliate is a prime disaster to the fry stage in large yellow croaker Larimichthys crocea. In the previous study, we have found that UBXN1 may be involved in scuticociliate disease resistance through genome-wide association analysis on the disease. In this study, we have identified UBXN1 gene and investigated its expression characteristics and related signal pathway. The complete cDNA sequence of UBXN1 was 915 bp encoding 304 amino acids. The putative UBXN1 protein is evolutionarily conserved and contains a UBA and a UBX domains. Moreover, UBXN1 has varying degrees of expressions in difference tissues, among which the highest expression is observed in brain followed by liver, heart and kidney, and the lowest expression in muscle through qPCR detection. It also showed that induced expression in spleen, brain, liver and kidney during the early phase of infection, and the expression gradually recovered to the control level at the late phase. Further subcellular localization analysis showed that UBXN1 uniformly distributed in cytoplasm and nucleus. In addition, we found 16 DEGs in a comparative transcriptome analysis between the UBXN1 overexpression group and control vector group, including up-regulated genes RPL41/RPL39/XIST/RNA45SN4 and down-regulated genes ATP8/ND4L. How UBXN1 does get in touch with these genes needs to be clarified in the upcoming studies. These findings collectively provide new insights finfish UBXN1 and its potential regulatory signaling pathway as well. To the best of our knowledge, no previous report on UBXN1 in fish.