The present invention is an active vaporization suction system and a controlling method thereof. The system includes a medication device and an active suction device. The medication device is detachably mounted on the active suction device. When a suction module is suctioned, a flow module outputs a launching signal to a control module. The control module outputs a vaporization current control signal to a power supply module according to the launching signal. The power supply module generates and outputs a Joule vaporization current to a Joule vaporizer of the medication device according to the vaporization current control signal, so that the Joule vaporizer vaporizes a liquefied medication in a vaporization chamber into a vapor medication. In this way, when the user actively sucks the suction module, the user can take the vapor medication for medical treatment, which increases an absorption rate of the vapor medication.