A method and a system for processing a data flow with an incomplete comparison process are provided. The method is implemented by a network device that includes a flow table and a flow filter in a memory thereof. A flow analyzing module is provided for analyzing and classifying packets of an input flow, and identifying an application category to which the input flow belongs. The flow table is queried according to a result of resolving the input flow for determining whether the input flow matches any flow entry of the flow table. The flow filter is queried if the input flow fails to match any flow entry of the flow table for determining whether features of the input flow match conditions of the flow filter. The input flow is processed accordingly, without needing to copy all flows that do not match the flow entries to the flow table.