The present invention relates to methods for dynamically detecting the interactions between various materials including bioactive molecules and for detecting target molecules. More specifically, the present invention relates to a method for dynamically detecting bait-prey interactions and a method for easily detecting target molecules which blocks or activates the interactions, the method comprising: allowing a material capable of forming a nano-assembly matrix, a bait and a prey to interact with each other, and analyzing whether a nano-assembly matrix is formed by the interaction between the bait and the prey in vitro or in vivo; or allowing a material capable of forming a nano-assembly matrix, a bait and a prey to interact with each other, inducing the formation of a nano-assembly matrix by a mediator (regulator) material in vitro or in vivo, and then analyzing whether the prey and the bait co-localizes on the nano-assembly matrix.