Starchy grain is usually supplemented to diets containing low-quality forage to provide sufficient energy for ruminant animals. Ruminal degradation of grain starch mainly depends on the hydrolysis of the endosperm, which may be variable among grain sources. This study was conducted to investigate the influence of endosperm structure of wheat and corn on in vitro rumen fermentation and nitrogen (N) utilization of rice straw. The 3×4 factorial design included three ratios of concentrate to forage (35:65, 50:50 and 65:35) and four ratios of wheat to corn starch (20:80, 40:60, 60:40 and 80:20). The endosperm structure was detected by scanning electronic microscopy and a confocal laser scanning microscopic. An in vitro gas test was performed to evaluate the rumen fermentation characteristics and N utilization. Starch granules were embedded in the starch–protein matrix in corn, but more granules were separated from the matrix in the wheat endosperm. With the increasing ratio of wheat, rate and extent of gas production, total volatile fatty acids, and ammonia N increased linearly (P<0.01), but microbial protein concentration decreased (quadratic, P<0.01), with the maximum value at a ratio of 40% wheat. The efficiency of N utilization decreased linearly (P<0.01). Rumen fermentation and N utilization were significantly affected by the concentrate-to-forage ratio (P<0.01). Significant interactions between the concentrate-to-forage ratio and the wheat-to-corn ratio were detected in total volatile fatty acids and the efficiency of N utilization (P<0.01). In summary, the starch–protein matrix and starch granules in the wheat and corn endosperm mixture play an important role in the regulation of rumen fermentation and N utilization under low-quality forage.