Recently, molecular communication (MC) has been studied as a micro-scale communication between cells or molecular robots. In previous works, the MC channels in unbounded environment was analyzed. However, many of the experimentally implemented MC channels are surrounded by walls, thus the boundary condition should be explicitly considered to analyze the dynamics of MC channels. In this paper, we propose a framework to analyze the frequency response of one-dimensional MC channels based on a diffusion equation with a boundary. In particular, we decompose the MC channel into the diffusion system and the boundary system, and show the relation between the cut-off frequency of the MC channel and the communication distance based on the transfer function. We then analyze the frequency response of a specific MC channel and reveal that the boundary can restrict the communication bandwidth of the MC channel.