The present invention provides a method of preparing a cross-condensed compound of an amino-acid derivative and (aminoalkyl) trialkoxysilane using microwave, including: irradiating and heating an amino-acid derivative and (aminoalkyl) trialkoxysilane in a microwave reactor to obtain a reaction product (step 1); and refining the reaction product obtained in the step 1 by removing an unreacted solid material from the reaction product and then leaving the reaction product at room temperature under vacuum to remove excess (aminoalkyl) trialkoxysilane therefrom (step 2). According to the method, since a cross-condensation reaction is performed using microwave, unlike a conventional condensation reaction, economic efficiency is increased due to no catalyst, short reaction time and no solvent. Further, the yield and selectivity of products is increased, and the condensation reaction can be environment-friendly performed because a solvent which can badly influence the environment may not be used.