Surface profile is one of the foremost aspects to evaluate milling performance. Its generation mechanism is affected by a variety of factors such as tool geometry, runout values, process parameters etc. and thus still deserves further investigation. This paper aims to propose a unified method to study the surface generation mechanism and to predict the machining quality for variable pitch tools considering runout. Firstly, a Floquet theory based algorithm is extended to analyze the machining stability and output the dynamic responses of the machining system. The resultant trajectories of cutting edges are obtained by kinematic synthesis of system vibrations, tool rotations and machining feed. Next, both the surface location error and the surface roughness are simultaneously extracted from the edge trajectories. A series of cutting tests are performed to validate the prediction results. Some new characteristics of the machined surface profile in terms of form errors and teeth marks are discovered and theoretically explained. Finally, the joint influences of tool geometry, runout values and process parameters on the surface generation mechanism and quality are analyzed in detail with the proposed method.