In order to discuss the etiolation mechanism and provide a theoretical basis in citrus breeding programs, we studied the relationship among photosynthetic characteristics, photosynthetic pigment content and the relative level of CgSGR expression of three graft combinations. Citrus grandis (L.) Osbeck. cv. ‘Hongmian miyou’ （Hm/Pt） and ‘Guanxi miyou’ grafted on Poncirus trifoliata （Gx/Pt）, and ‘Hongmian miyou’ grafted on C. junos (Hm/Cj) were used as the experimental materials. The results were showed as follows. (1) The photosynthetic rate, stomatal conductance, transpiration rate and mesophyll carboxylation efficiency of Hm/Pt were significantly lower than that of Gx/Pt and Hm/Cj; (2) The three graft combinations had similar change trend of chlorophyll content, while the chlorophyll a, b and total chlorophyll in Hm/Pt were significantly lower than that of control groups; (3) The open reading frame (ORF) of CgSGR was 816 bp, encoding 271 amino acids (GenBank accession number: MF945620). The deduced protein molecular weight was 30.62 kD, which was a stable alkaline hydrophilic protein. According to multiple sequence alignment analysis, the sequence of ‘Hongmian miyou’ and ‘Guanxi miyou’ were high consistency with C. grandis, C. sinensis and C. clementina. Based on phylogenetic tree analysis, CgSGR keep closest genetic relationship with C. grandis, C. sinensis and C. clementina, and relatively close with Litchi chinensis; (4) RTqPCR results showed that CgSGR expression levels were upregulated in Hm/Pt when the plants initiated etiolation. The CgSGR transcripts reached the highest level grafted after 404 days; (5) With the growth of the grafted seedlings, the trend of expression level of CgSGR was opposite with the net photosynthetic rate and chlorophyll content. The results indicated that CgSGR might be involved in transcriptional regulation during the seedling etiolation of C. grandis ‘Hongmian miyou’ grafted to P. trifoliata.