This invention discloses a circuit encoding method and a circuit structure recognition method. The circuit encoding method is applied to a circuit structure recognition process of a circuit. The circuit is coupled to a voltage source and a reference voltage. The circuit encoding method includes: selecting a target transistor from the circuit; when a terminal of the target transistor is electrically connected to the voltage source or the reference voltage, adding a first value to a terminal value of the terminal; when the terminal of the target transistor is electrically connected to a terminal other than the voltage source and the reference voltage, adding a second value to the terminal value of the terminal; and taking a set of multiple terminal values of the target transistor as a transistor signature of the target transistor.