The present invention relates to a system for analyzing molecular sequences, which is capable of decoding unit molecules constituting various biopolymers on a real-time basis using nanochannels. A control electrode serves to control the unit molecules passing along the channel such that the velocity of movement, arrangement, and directivity of the unit molecules can be rendered uniform. Particularly, at least four probe electrodes are separately formed in the case of decoding ss-DNA base molecules. Each probe electrode is coated with four different types of DNA base molecules to maximize detection efficiency through the interaction with complementary base molecules moving along the inside of the channel.