The invention discloses a data processing method based on a multilayer information united index. The method comprises the steps that a data transmission data index comprising virtual channel frame counts, virtual channel identifiers and frame time is extracted from original data; virtual channel data is extracted according to the data transmission data index, and a virtual channel data index comprising the virtual channel frame counts, the virtual channel identifiers and the frame time is established; source packet data is extracted according to the virtual channel data index, and a source packet data index comprising the virtual channel frame counts, source packet counts, source packet identifiers and source packet time is established; and sequencing, splicing and repetition-removing operation are performed on the source packet data according to the source packet data index to generate continuous and complete source packet data. Through the method, the problem that the data with identical virtual channel frame counts and source packet counts will be deemed as repeated data and removed through traditional methods is avoided, the continuity and completeness of the data are guaranteed, and the processing demand of space science on satellite sounding data can be met.