With high rates of food and nonrenewable fossil fuel consumption worldwide, we are facing great challenges in ensuring food and energy security to satisfy the world population. Intercropping, as an important and sustainable cropping practice in agroecosystems, has been widely practiced around the world. Many studies have shown that some plants can deliver high yields when intercropped with other plants. Here, we review the biological mechanisms in improving resource utilization efficiency and illustrate the practical application of intercropping in ensuring food and energy security through improving production. Identifying suitable energy plants for marginal land, land not suitable for food crops growth, is an effective strategy to acquire high production of bioenergy, thus removing competition between the use of land for food and energy. The effective application of intercropping provides a potential pathway for production of food crops and energy plants by improving resource use efficiency and resistance to environmental stress.