Based on misunderstandings and countermeasures of comprehensive budget management in geological exploration company, concrete analysis was conducted from misunderstanding, lack of effective organization system support, poor executive force, control and performance evaluation mechanism, establishing comprehensive budget oriented scientific management was proposed, a reasonable system of multi-level budget management organization system to establish strict perfect budget implementation and control system was advised, the budgetary control evaluation analysis system and a series of countermeasures need to be improved, which would provide a basis for the comprehensive budget management work smoothly for geological exploration company.