In a water-level-fluctuating zone (WLFZ) of the Three Gorges Reservoir, vegetation restoration is challenged not only by submersion for long periods, but also by sand deposition, drought, and other factors. To study the influence of sand burial and drought on the germination and growth recovery of Cynodon dactylon in a WLFZ of the Three Gorges Reservoir, C. dactylon was transplanted and buried in sand of several particle sizes at various depths after anti-seasonal flooding. Germinating seedlings of C. dactylon in the WLFZ could not penetrate sand layers deeper than 8 cm with a particle size of less than 1.25 mm. Sand burial significantly decreased the emergence rate of C. dactylon. As burial depth increased, the emergence rate dropped sharply; at the same burial depth, the emergence rate significantly increased as particle size decreased. Plant height and leaf length were significantly inhibited as the burial depth increased and the particle size decreased The plant height, leaf number, and leaf length of buried plants were significantly smaller than those of controls. As stress time increased, drought and sand burial significantly decreased plant height, leaf number, leaf length, and leaf width. The photosynthetic electron transport rate decreased significantly and the heat dissipation rate increased significantly as burial depth increased and particle size decreased. Combined stress of sand burial and drought significantly decreased the photosynthetic electron transport rate and heat dissipation ability in the treatment groups compared to control groups; combined stress also significantly decreased the photosynthetic ability of treated plants, and resulted in them being easily damaged by high light intensity in the summer. Thus, annual flooding significantly decreased the endurance of C. dactylon for sand burial and drought in the Three Gorges Reservoir. The ability of C. dactylon for growth recovery was significantly reduced as particle size decreased and the burial depth increased under conditions of sand burial and drought. These conditions would lead to more rapid population decline of C. dactylon in WLFZs of the Three Gorges Reservoir.