The invention discloses film coating equipment and a method for flexible substrate thick film coating. The film coating equipment comprises an unrolling chamber, an ion treatment chamber, multiple film coating chambers and a rolling chamber, wherein the unrolling chamber, the ion treatment chamber, the film coating chambers and the rolling chamber are connected in sequence; the ion treatment chamber and the film coating chambers are distributed on the periphery of a film coating water-cooling roller, and the unrolling chamber and the rolling chamber are arranged on the two sides of the film coating water-cooling roller separately; and the film coating chamber located in the middle is provided with a continuous evaporation coating source, and intermediate-frequency magnetic control targets are arranged in the rest of the film coating chambers. The method comprises the steps that after ion treatment of flexible substrates is finished, the flexible substrates are fed into the film coating chambers in sequence along with rotation of the film coating water-cooling roller, firstly at least one-time sputter coating is conducted on the surfaces of the flexible substrates through the intermediate-frequency magnetic control targets, then evaporation coating is conducted on the flexible substrates through the continuous evaporation coating source, at least one-time sputter coating is carried out on the surfaces of the flexible substrates through the intermediate-frequency magnetic control targets, and finally the flexible substrates are sent out. According to the film coating equipment and the method, coating of flexible substrate surface thick film layers can be achieved, the film coating efficiency is high, and the film layer surface evenness is also high.