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Based on obtaining <i>mstnb</i> gene knockout in <i>Pelteobagrus fulvidraco</i>, a study on the effect of the <i>mstn</i> gene on skeletal morphology and growth was performed by comparing the number and length of the vertebrae of mutant and wild-type fish in a sibling group of <i>P. fulvidraco</i>, combined with the differences in cells at the level of vertebral skeletal tissue. It was found that <i>mstnb</i> gene knockdown resulted in a reduction in the number of vertebrae, the length, and the intervertebral distance in <i>P. fulvidraco</i>, and these changes may be the underlying cause of the shorter body length in mutant <i>P. fulvidraco</i>. Further, histological comparison of the same sites in the <i>mstn</i> mutant and wild groups of <i>P. fulvidraco</i> also revealed that the number and density of osteocytes were greater in <i>mstnb</i> knockout <i>P. fulvidraco</i> than in wild-type <i>P. fulvidraco</i>. Our results demonstrated that when using genome editing technology to breed new lines, the effects of knockout need to be analyzed comprehensively and may have some unexpected effects due to insufficient study of the function of certain genes.