Populus yunnanensis Dode., a native dioecious woody plant in southwestern China, was employed as a model species to study sex-specific morphological, physiological and biochemical responses to elevated CO2 and salinity. To investigate the effects of elevated CO2, salinity and their combination, the cuttings were exposed to two CO2 regimes (ambient CO2 and double ambient CO2) and two salt treatments in growth chambers. Males exhibited greater downregulation of net photosynthesis rate (Anet) and carboxylation efficiency (CE) than females at elevated CO2, whereas these sexual differences were lessened under salt stress. On the other hand, salinity induced a higher decrease in Anet and CE, more growth inhibition and leaf Cl− accumulation and more damage to cell organelles in females than in males, whereas the sexual differences in photosynthesis and growth were lessened at elevated CO2. Moreover, elevated CO2 exacerbated membrane lipid peroxidation and organelle damage in females but not in males under salt stress. Our results indicated that: (1) females are more sensitive and suffer from greater negative effects than do males under salt stress, and elevated CO2 lessens the sexual differences in photosynthesis and growth under salt stress; (2) elevated CO2 tends to aggravate the negative effects of salinity in females; and (3) sex-specific reactions under the combination of elevated CO2 and salinity are distinct from single-stress responses. Therefore, these results provide evidence for different adaptive responses between plants of different sexes exposed to elevated CO2 and salinity.