The invention discloses an extraction method for influence factors of carbon exchange of an ecosystem and a system. The extraction method includes steps of 1), acquiring attribute data of carbon flux samples in a carbon flux data observation station; 2), inputting the attribute data, which are obtained in the step 1), of the carbon flux samples, selecting the optimal combination by the aid of proposed fuzzy rough and reduction integrated algorithm of shuffled frog leaping or quick fuzzy rough and reduction integrated algorithm based on importance, and finding an environmental factor set with the closest relationship with carbon flux; and 3), realizing modeling and stimulating for various environmental factors in the environmental factor set obtained from the step 2) by the aid of a neural network, and obtaining extraction rate of the environmental factors of the carbon flux. The extraction system comprises a data import module, a factor extraction module, an input module and an evaluation module. By the aid of the extraction method and the system, the range of correlation factors of the carbon flux in the researched ecosystem can be effectively reduced, research efficiency is improved, and inherent law among the environmental factors is found.