The invention discloses a control method for gluconate production by a microbiological method. A high-yield gluconic acid strain is adopted as an original strain, which is moved into a fermentation tank for fermentation production of gluconate after seed culture. During fermentation, according to an on-line respiratory quotient (RQ), the adding speed and adding amount of glucose can be controlledin real time. The control method of the invention can make the glucose consumption rate reach 12g/L/h, and the conversion rate of production in the fermentation tank reach over 110%, thus realizing automatic flow feeding and substantially reducing the production cost.