A battery system, a control method of a cell balance procedure and a calculation method of a balance charge capacity are provided. The battery system includes a plurality of battery units, a communication bus and a host control unit. Each battery unit includes a plurality of cells, an isolated charger, a switch array circuit, a balance slave switch and a balance slave controller. The host control unit includes a balance host controller, a balance host switch and a system current measurement unit. When the error between a balance detection voltage calculated by each balance slave controller and the balance detection voltage calculated by the balance host controller is less than a predetermined value, the balance host switch and the corresponding balance slave switches are in conduction and the specified plurality cells of battery system are charged for keeping cell balance purpose.