The invention discloses a load balancing control method and system of message queues, which are used for improving the flexibility of load balancing control of the message queues and ensuring that a client side flexibly switches the message queues. The load balancing control method of the message queues comprises the following steps of: polling the current depth of each message queue, and generating alarm information when overload message queues about that the current depth is up to a preset queue depth alarm threshold value exist, wherein the alarm information contains identification information and the current depth of each overload message queue; respectively determining the amount of business service required to be increased for each overload message queue according to the current depth of each overload message queue in the alarm information and the average handling ability of the business service; and selecting a corresponding amount of business service meeting an allocation condition, and increasing the overload message queues indicated by the identification information allocated to each overload message queue in the alarm information.