The MKK3-p38 MAPK pathway has been reported to mediate larval settlement in Amphibalanus (=Balanus) amphitrite. To clarify the underlying molecular mechanism， we applied label-free proteomics to analyze changes in the proteome of cyprids treated with a p38 MAPK inhibitor. The results showed that the expression levels of 80 proteins were significantly modified (p < 0.05). These differentially expressed proteins were assigned to 15 functional groups according to the KOG database and 9 pathways were significantly enriched. Further analysis revealed that p38 MAPK might regulate the energy supply and metamorphosis. Two potential regulatory proteins， CUB-serine protease and PKAα， were both down-regulated in expression. CUB-serine protease localized to postaxial seta 2 and 3， as well as the 4 subterminal sensilla in the antennule. Importantly， it was co-localized with the neuron transmitter serotonin in the sections， suggesting that the CUB-serine protease was present in the neural system. PKAα was highly expressed during the cyprid and juvenile stages， and it was co-localized with phospho-p38 MAPK (pp38 MAPK) to the cement gland， suggesting that PKAα might have some functions in cement glands. Overall， p38 MAPK might regulate multiple functions in A. amphitrite cyprids， including the energy supply， metamorphosis， neural system and cement glands.