The invention relates to a flow path control system and method of an automatic analyzer. A first multi-way valve and a second multi-way valve are arranged for cooperation, when liquid is pumped into a reaction container from a corresponding liquid storage container or liquid is pumped into a corresponding liquid storage container from the reaction container, branch pipelines of the first multi-way valve can be kept to be communicated with the liquid storage container all the time, the first multi-way valve connected with the liquid storage container does not need to be switched many times, the conversion rate of the first multi-way valve is easily reduced, the service life of the system is prolonged, and maintenance cost is reduced. Besides, after the liquid in the liquid storage container is pumped, liquid in the branch pipelines connected with the liquid storage container can return to the portion below the first multi-way valve, accordingly when the first multi-way valve is switched later, no liquid exists in the branch pipelines of the first multi-way valve and an interface at a public end, cross pollution of the liquid in the branch pipelines and the liquid in the public end can be avoided, and analysis precision is easily improved.