Photosynthetic and transcriptomic characteristics of a chlorophyll (Chl) b-deficient mutant type 2b rice (ch14) were investigated in this study. The ultrastructure of chloroplast in ch14 demonstrated irregular chloroplast enhancement (loss of starch granules, indistinct membranes, and thinner grana). Ch14 had significantly lower carotenoid, Chl a, Chl b, and total Chl contents, but a higher ratio of Chl a to Chl b than a wide-type rice. 3,594 genes were differentially expressed in ch14, among which 309 transcription factors were related to Chl degradation and biosynthesis, chloroplast formations, and the photosynthesis capacity. PsbR, GSA-AT, PBGD, PPOX, MgMT, and POR genes were down-regulated, reducing Chl content and photosynthetic capacity in the ch14. This study suggests that Chl degradation may be attributed to abnormal chloroplast development and down-regulation of gene expression in the common pathway and Mg branch and the rise in Chl a to Chl b ratio may be involved in the alternative Chl b degradation pathway.