Two-dimensional gel electrophoresis was used to gain a further understanding of the molecular mechanisms involved with flower bud differentiation in Crocus sativus L. A total of 101 proteins exhibited significant differential expression, and 72 proteins were reliably identified. During the process of flower bud differentiation in Crocus sativus L., FBA, TPI, NSE, enolase, LOS2, MDH and succinyl-CoA ligase, provided adequate energy and nutrition to complete flower bud differentiation. Methionine-tRNA ligase and arginine may likely interact with phytohormones and signalling molecules. A number of regulatory and antioxidant-related proteins, such as HSP, chaperonin, APX, CAT, GME, Trx and TpxII, transferred defense related signal molecules in response to various stresses. Several proteins associated with cytoskeleton and protein metabolism, also revealed a higher abundance, including proteins that were critical for fiber development. In conclusion, our results provide novel insights into the molecular basis for flower bud differentiation in Crocus sativus L. PRACTICAL APPLICATIONSCrocus sativus L. is known as "plant gold," and has always been used as a flavor and color in foods, as well as a dye. In the production of Crocus sativus L., flowers are the principal products. At present, florescence of Crocus sativus L., which to be handly picked, is too concentrated and the gradual deterioration of flower quality restrict the development of Crocus sativus L. industry. In this study, the biological functionalities and molecular mechanisms of some key proteins that involved for flower bud differentiation were detected and identified by proteomics analysis. This study laid a theoretical basis for the temporal regulation of blooms, selective breeding and the control of gene regulation in the active biosynthetic components of stigmas. An improved understanding of the impact of key proteins during flowering could potentially provide further scope for optimizing Crocus sativus L. industry.