The present disclosure relates to compensating method for cell assembly. According to a deviation value of a key position of a measured array substrate, a compensation value of an exposure parameter of black matrix process of a color film substrate is calculated in real time by using historical measurement data of batches. The compensation value is fed back to a manufacturing apparatus in real time. The manufacturing apparatus corrects the key parameter of the apparatus timely according to the compensation value of the exposure parameter of the black matrix, to manufacture a color film substrate matching with the array substrate.