The carotenoids start the inner membrane structures (IMS) transformation of chloroplasts during colour transformation in tomatoes, but the mechanism remains unclear. E-2-hexenal (E2H) may function downstream of carotenoids to regulate the transformation. In the tomatoes treated with E2H, colour transformation was inhibited and the colour transformation cannot be initiated by ethylene (ET) again, whereas in the ET pretreated tomatoes, the E2H lost the function of inhibition. Therefore, the E2H function downstream of ET. The electron micrographs showed the exogenous E2H accelerated the IMS transformation before enough carotenoids accumulated. Therefore, the E2H may acted downstream of the carotenoids starting the IMS transformation. The contents and the biosynthesis locations of chlorophyll, lycopene and β-carotene supported the E2H accelerated IMS transformation. The E2H expedited LOXC expression caused advanced free linolenic acids consume, E2H also accelerate the release of linolenic acids directly, thus the composition changes altered the IMS. The HPL expression patterns may related with the endogenous E2H feedback balance. The titratable acids, ascorbic acids, soluble solids and malondialdehyde contents also supported the hypothesis. Above all, E2H mediated the carotenoids started IMS transformation. Novel function of the E2H was proposed. Keywords: tomato, E-2-hexenal, chloroplasts, chromoplast, plastids, colour, carotenoid