The paper takes the rural habitat environment under the epidemic as the research object with the purpose to explore how to improve and optimize its governance for a better rural habitat and a beautiful countryside. Although the governance of rural habitat environment has been implemented in the recent years, some practical problems still remain unsolved. After reviewing how the foreign countries perform governance and how the epidemic impacts the governance, by putting the current situation of rural habitat environment governance into consideration, and through the in-depth interpretation with respect to rural domestic waste, sewage treatment, infrastructure construction, management mechanisms and subject loss, the paper proposes the strategies for optimization and the paths to govern habitat environment. Based on the combination of epidemic prevention and strategies for rural habitat environment governance, a valid path to govern the rural habitat environment is scientifically planned, and a safe and healthy living environment for rural residents is under the solid and steady construction to help promote the further development of China's new countryside and the implementation of rural revitalization strategy.