The COVID-19 pandemic introduced risks and challenges to global food and nutrition security. In this paper, we examine the impact of the COVID-19 pandemic on the nutritional intake of China’s rural residents using panel data and a fixed effects model. The data were collected in 2019 and 2020 and covered nine provinces and 2631 households in rural China. The results reveal that an increase of 100 confirmed cases in a county resulted in a 1.30% (p < 0.01), 1.42% (p < 0.01), 1.65% (p < 0.01), and 1.15% (p < 0.01) decrease in per capita intake of dietary energy, carbohydrates, fats, and proteins, respectively. Moreover, the COVID-19 pandemic had a significant and negative effect on dietary macronutrient intake in the low-income group at the 5% level of significance. Our study indicates that the potential insufficient nutrition situation, nutritional imbalance, and dietary imbalance of low-income rural residents should be addressed appropriately.