A crankshaft rotating angle controlling method and a crankshaft rotating angle controlling system are provided. A shut-off signal is obtained, and an engine speed is judged. If the engine speed is lower than a specific value, a generator is set in a driving mode at an ending point of a missing tooth signal in a gear pulse signal, such that the generator in the driving mode drives a crankshaft to exceed a top-dead-center of a cylinder. When the crankshaft arrives at a bottom-dead-center of the cylinder, the generator is set to be in a holding mode of an error phase of a three-phase current. Through the generator in the driving mode, the given error phase of the three-phase current stops the generator immediately and the crankshaft is fixed within an angle range of a default stop position.