The invention discloses a capital clearing management system and method for a multi-merchant business platform. The capital clearing management system comprises a platform order management module, a capital clearing module and a platform merchant module, wherein the platform order management module comprises an order splitting unit for splitting the orders of merchants according to different merchants and an order classifying unit for classifying all orders of the same merchant; the capital clearing module comprises an order capital checking unit for checking the order capitals of each shop, a capital settlement unit for settling the capitals and an automatic capital transferring unit for automatically transferring the capitals into the accounts of the corresponding merchants; and the platform merchant module comprises an automatic merchant capital posting unit for automatically receiving the capitals. According to the invention, the orders of the users can be automatically split and classified according to the merchants; and automatic capital transfer and posting for different merchants are realized through order capital checking, so that the settlement intervals of platform merchant capitals are shortened, and the clearing is automatically carried out.