An in situ IR technique was applied in the selective synthesis of the key intermediate for rapamycin derivatives, which made the reaction endpoint easily defined. This technology solved a bothersome problem in the preparation of rapamycin derivatives, and based on this technique, the 31-OH and 42-OH of rapamycin were chemically modified by a series of quaternary ammonium salts to generate 11 compounds. The solubility of all these compounds was remarkably improved (25,000 times higher than that of rapamycin) and their structures were confirmed by MS, IR, 1D and 2D NMR techniques.