Disclosed are an ultra-high sensitivity target signal detection method based on analysis of a noise signal of a sensor using deep learning based anomaly detection and a system using the same. More particularly, disclosed are a method and apparatus for receiving a noise signal from a sensor and inputting data to an artificial neural network trained with a normal noise signal to determine whether or not a target signal is present. The target signal detection method is capable of detecting a target signal having a very low concentration that can be detected by a conventional sensor, whereby the target signal detection method is useful in developing an ultra-high sensitivity sensor.