The invention discloses compact type flexible substrate magneto-controlled sputter coating equipment and method. According to the equipment, a partition clapboard is arranged in a vacuum chamber, space in the vacuum chamber is divided into a winding area and a coating area, the partition clapboard is provided with a through hole for a flexible substrate to pass through, the flexible substrate penetrates the whole vacuum chamber, a heater and an ion source are arranged in the winding area, a magneto-controlled sputter device is arranged in the coating area, multiple unit clapboards are arranged in the coating area, and space in the coating area is divided into one flexible substrate conveying unit and multiple coating units. According to the method, the winding area and the coating area in the vacuum chamber are vacuumized, and the flexible substrate unwound by an unwinding roller passes through the winding area firstly, and is subjected to ion treatment and preheating in the winding area, then conveyed into the coating area, subjected to sputter coating through the multiple coating units in sequence and finally conveyed to the winding area to be wound through a winding roller. The equipment is compact in structure, saves equipment cost and can effectively prevent work atmospheres of the different process stages from influencing one another.