The proportion of rural energy consumption is gradually expanding, and it has also become a region that cannot be ignored for energy system transformation and carbon emission reduction. In order to increase the utilization rate and economic benefits of biogas project, this paper applies biogas hydrogen production technology to a rural integrated energy system. An operation strategy and three performance indicators are introduced for participating the system in the electricity market and hydrogen market. The result of a case study shows its performance improvement. Compared with trading in the electricity market only, hydrogen production helps the rural integrated energy system to increase energy efficiency and operation profit. In addition, the sensitivity analysis shows that the cost of biogas fermentation and the price of hydrogen production are the main factors affecting its profit cost ratio.