To uncover the underlying mechanism of temperature-responsive flowering in Crocus sativus and unveil flowering regulatory proteins, iTRAQ (isobaric tags for relative or absolute quantitation)-based proteomics were applied to study the differences in protein expression profiles in flowering and non-flowering saffron grown at room- and low-temperatures, respectively. A total of 5,624 proteins were identified，and 201 proteins showed differential accumulations between the flowering and non-flowering groups.