The present disclosure relates to a method for discovering effective bioactive compounds, based on plant developmental biology, and aims to discover a lead bioactive compound for new drugs by repeating screening based on phenotypes of a plant as a marker on the basis of plant developmental biology. To this end, the present disclosure provides a method for discovering effective bioactive compounds, and includes screening candidates for developing a new drug by using unique phenotypes as a marker shown by a plant when it is grown with a specific material.