Abstract: The significantly negative impact of marine invasive species underscores the need to understand the dynamics of invasion success. MicroRNAs (miRNAs) play a crucial role in regulating gene expression in response to stresses during invasions. Using the invasive tunicate Ciona robusta as a model, here we aim to study intragenic miRNA–host gene co-expression and functional regulation in response to recurrent salinity challenges. Despite genomic nestedness, only 9% of miRNA–host gene pairs showed significant co-expression (p < 0.05, correlation coefficient > 0). Recurring stresses dynamically altered the co-expression, revealing distinct miRNA–host gene expression at different stress times and stages. These differentially expressed miRNAs (p_adj < 0.05, |log₂foldchange| > 1) regulated biological processes, including free amino acid metabolism, water channel function, and ion transport to maintain osmotic homeostasis. These functional regulations were specific to time and stage, targeting the same type of osmolytes through varied pathways. Our findings highlight the diverse regulatory roles of miRNAs in enabling rapid responses to environmental stresses during invasions, providing new insights into miRNA-driven phenotypic plasticity under changing conditions.