Abstract: Lignocellulosic structural changes of Spartina alterniflora before and after anaerobic fermentation under mesophilic conditions (35℃) were characterized by scanning electron microscopy (SEM), Fourier transform infrared (FTIR) spectroscopy and X-ray diffractometer (XRD). The results of SEM microphoto analysis indicated that vascular bundle in stem of S. alterniflora was easily biodegradable tissue compared with parenchyma cell. The analyses of FTIR spectra showed that ratios of the intensity of characteristic peak of lignin to that of carbohydrate for S. alterniflora after anaerobic fermentation were more than twice as much as those of the undigested one. Crystallinity index of S. alterniflora cellulose dropped from 0.510 before fermentation to 0.479 after fermentation, as indicated by XRD results. It can be concluded that the shielding effects of lignin on cellulose and hemicellulose and the crystalline cellulose are the main factors of inhibiting anaerobic bioconversion of S. alterniflora.