The invention relates to an analysis method for researching formation of variegation of nelumbo nucifera based on combination of transcriptomics with proteomics TMT, and provides a new method for disclosing a molecular mechanism of the formation of the variegation of plants. Samples of "Dasajin" nelumbo nucifera petals are collected, through transcriptome Illumina HiSeq sequencing, expression difference genes on an anthocyan metabolic pathway are screened, besides, proteins in the samples are extracted, the concentration of the proteins is determined, the quality is detected, through TMT labelmarking and 2D-LC-MS analysis, bioinformatics analysis is performed through combining with the proteomics, the proteins for adjusting and controlling expressing level differences on the anthocyan metabolic pathway are screened, the genes having differences in the transcriptome are related into the proteomics, and key proteins and corresponding genes for adjusting and controlling the variegation of "Dasajin" nelumbo nucifera are screened, so that the purpose of understanding a manner of the proteins and the genes for adjusting the formation of the variegation of the "Dasajin" nelumbo nuciferais achieved, and a new thinking and a new method are provided for the formation mechanism of the variegation of other plants.