Compared with the sectional roller flatness meter, the integral roller flatness meter is more suitable for products with higher requirements on surface quality, and thus becomes the trend of the contact-type flatness meter for cold rolling. Due to its structure design, some problems arise. Under the action of the dead weight or an external load, the deflection deformation of the roller changes the stress state of the sensor installed inside it and generates an additional signal. This paper studies the mechanism of the signal and the recognition and elimination method. First, according to the structure of the detection roller and the connection mode of the sensors, the ideal waveform characteristics of the flatness signal are analysed. Through an experiment on the 650 mm integral roller flatness meter platform, the ideal waveform and actual waveform characteristics are compared, and the influence of the additional signal on the detection signal is analysed. Then, according to the deflection deformation of the roller and its corresponding stress distribution characteristics, the generating mechanism of the additional signal is revealed. Finally, a minimum error method is proposed, which ensures the elimination of the deflection influence on all detection units in real time. During the process of flatness detection, the zigzag feature of the flatness distribution curve is eliminated; thus, during the process of flatness control, the bad influence of the roller deflection is removed. The industrial application shows that the work presented in this paper can obviously improve the products quality.