A peripheral component interface-express (PCI-E) standard selection setting system and microserver are disclosed, in which a selection controller selects an arrangement setting in storage elements to arrange the PCI-E control chip, whereby each of the second PCI-E standard ports is or is not arranged as an upstream PCI-E standard port, so that a single PCI-E standard control chip may arrange one of the multitude of PCI-E standard ports as an upstream PCI-E standard port, so that the upstream PCI-E standard port may have a data transmission with one of the multitude of system on chips (SOCs) connected with the PCI-E standard control chip.