The invention discloses a comprehensive pretreatment method for shaft penetration in a mined-out area stratum. The method comprises the steps that (1) treatment drilling holes are formed around the center of a proposed shaft and are formed on the periphery of the proposed shaft; (2) filling materials are conveyed to a mined-out area through the treatment drilling holes on the ground. According to the comprehensive pretreatment method for shaft penetration in the mined-out area stratum, mined-out area dangers during shaft construction can be effectively avoided, the milled-out area is pre-treated before the shaft is excavated, and shaft excavation construction safety and built shaft running safety are ensured.