The invention discloses cyclo(lle-lle) dipeptide and a preparation method thereof. The cyclo(lle-lle) dipeptide is obtained by fermenting and separating a paecilomyces variot bainier strain SJ1 isolated from wild sea-buckthorn. The invention further provides application of the cyclo(lle-lle) dipeptide in promoting crop seed germination, improving the salt tolerance of crops, inducing flowering ofthe crops, resisting downy mildew of cucumber and improving the frost resistance of the crops. The strain is easy to culture, and a cyclodipeptide compound can be separated and purified from a fermentation solution by a relatively simple method. The compound has no pollution to the environment, has short production cycle, high activity and extremely low production and use cost, and is easy to produce in a large scale in batch. The cyclodipeptide compound has an obvious promoting effect on the crop seed germination and has remarkable effects in the aspects of salt resistance, flowering induction, cucumber downy mildew resistance, freezing resistance, yield increase and fertilizer utilization. The compound has good development value and good application prospects.