The invention provides a flow cytometry bus control device. The flow cytometry bus control device is characterized by comprising a sensor unit, a data acquisition unit, a PCI-E interface unit, a lower computer interface unit, a main control unit and an upper computer data receiving unit. The sensor unit converts received optical signals into electric signals according to a certain corresponding relation; the data acquisition unit conditions the electric signals output by the sensor unit, converts analog signals into corresponding digital signals, finally extracts pulse parameters representing cell characteristics and then sends data to an uplink in the form of a PCI-E bus protocol; the PCI-E interface unit achieves a topological structure of a PCI-E bus, increases the number of PCI-E interfaces and achieves PCI-E bus connection between the main control unit and the data acquisition unit and the lower computer interface unit.