National forest inventory (NFI) is an important work for the country to keep track of the status quo and dynamic of forest resources at the macro level.In order to make NFI meet the demand of daily management of nature reserves, we optimize the survey factors, methods, and record forms for the forest inventories, taking into account the characteristics of nature reserves in China. Several investigation factors are revised or added, including total species, plant abundance, plant viability, and number of live animal individuals, traces, nests or lairs. Investigation and statistical methods for understory, vegetation and natural regeneration, as well as field investigation record forms are improved. The new methods were tested on the NFI fixed sample plots in six nature reserves in Beijing in July and August 2015. The results indicate that the amount of biodiversity increased significantly. The average number of recorded shrubs and herbaceous species in each plot increased by 150% and 700%, respectively. It is indicated that the improved methods can provide a better knowledge of the current conditions of the biodiversity and forest ecosystem in nature reserves. We hope these methods can be applied in the future national forest inventories.