To explore the molecular response of fish larvae to nutritional manipulation, the partial sequences of bone morphogenetic protein (BMP1, BMP2, BMP4, BMP5, and BMP10) genes were obtained, and their expressions were quantified on golden pompano Trachinotus ovatus at 28 days post hatching. Artemia nauplii were separately enriched with Nannochloropsis and Algamac 3080, and non-enriched Artemia nauplii were used as a control feed. The lowest jaw deformity rate occurred in fish fed Algamac 3080 enriched Artemia nauplii. The expression level of BMP4 of fish fed Algamac 3080 enriched Artemia nauplii was significantly lower than those fed Nannochloropsis enriched and non-enriched Artemia nauplii. The lowest expression level of BMP10 was found in fish fed non-enriched Artemia nauplii, and the highest expression of BMP10 was observed in fish fed Algamac 3080 enriched Artemia nauplii. Correlation analysis indicates that nutritional manipulations can significantly affect the expression level of BMP4 and BMP10 genes. The concentration of dietary docosahexaenoic acid (DHA) can significantly affect the expression level of BMP10. This study indicates that the use of Algamac 3080 enriched Artemia nauplii results in fast fish growth and low jaw deformity, and BMP4 and BMP10 gene expressions were closely related to jaw deformity in golden pompano larvae.