Salmonids, classified as physostomous fish, maintain buoyancy by ingesting air to inflate their swim bladders. Long-term submergence has been shown to cause body imbalance and reduced growth performance in these fish. Previous studies have demonstrated that extended photoperiod can promote growth in salmonids. This study aimed to investigate the regulatory effects of prolonged lighting on the growth of submerged rainbow trout (Oncorhynchus mykiss) by examining the transcriptional expression of genes in the growth hormone (GH)-insulin-like growth factor (IGF) axis. Rainbow trout were individually reared in one of the six environments, defined by the combination of three photoperiods (0L:24D, 12L:12D, and 24L:0D) and two spatial rearing modes (routine and submerged), for 16 weeks. We compared the growth performance of rainbow trout in different environments and further analyzed the transcription profiles and correlations of GH-IGF axis genes in the brain, liver, and muscle. The findings of this study were as follows: growth performance of rainbow trout gradually increased with photoperiod duration. Specifically, final body weight (FBW) and specific growth rate (SGR) increased, while feed conversion ratio (FCR) decreased. Extended photoperiod partially mitigated the adverse effects of long-term submergence on rainbow trout growth. Under 24L:0D photoperiod conditions, growth performance (FBW, SGR, and FCR) in submerged and routine rainbow trout was more closely aligned compared to 0L:24D and 12L:12D photoperiod conditions. In response to variations in the photoperiod, GH-IGF axis genes of rainbow trout exhibited significant transcriptional differences, particularly between treatments with 0L:24D and 24L:0D light exposure. An extended photoperiod facilitated the restoration of the expression of GH-IGF axis genes in submerged rainbow trout towards routine levels, including the up-regulation of sst and sstr2 genes in the brain. Correlation analysis implied differentiation of physiological functions of ghr and igfbp paralogs. This study provided insights into the feasibility of enhancing the growth performance of submerged salmonids through photoperiod manipulation.