Phenotypic plasticity and symbiosis are two key factors influencing the evolution and adaptation. However, knowledge of how symbiotic cells and organs evolve under and adapt to emerging environmental changes is still scarce. Herein, we assessed the long-term phenotypic changes of gill in aposymbiotic deep-sea mussels induced by methane deprivation to clarify the physiological basis that facilitates evolution and adaptation of mussels. We showed that aposymbiotic mussels managed a long survival by digesting symbionts and remodeling the global metabolism to conserve energy. The mussels also replaced bacteriocytes with ciliated cells to support filter-feeding, and retained robust generation of new cells to dynamically respond to environmental changes. These phenotypic changes were regulated by sterol-related signaling pathway of host and influenced by sterol metabolism of symbiont. The robust plasticity of gill advantages the evolution and adaptation of deep-sea mussels, and highlights the interaction between environment and symbiosis in the complex evolution of holobionts.