In 2012 the Ministry of Agriculture of China launched a project exploring Nationally Important Agricultural Heritage Systems (China-NIAHS). Through two rounds of applications and selection in 2012 and 2013, 39 traditional agricultural systems were selected and designated as China-NIAHS, including 19 forestry systems, 14 planting systems, four agricultural complex systems and two other systems. From a system origin perspective there were 24 agricultural systems, some dating back 1000 years. Twenty heritage systems are located in areas inhabited by ethnic minorities. Agricultural heritage systems face general challenges, such as ecosystem degradation and destruction, loss and abandonment of traditional agricultural technologies and landscapes, lagging agriculture scale and industrialization, and limited farmer benefit-sharing and incentives. Compared to other types of heritage, the conservation and development of agricultural heritage systems is more complex and difficult. In order to achieve sustainable development of agricultural heritage systems, the government should play a leading role and improve financial support functions. Local people should also explore market-oriented approaches and adaptive management methods on protection and development of NIAHS. Multi-participation and benefit-sharing mechanisms should be established and basic research needs to be strengthened.