The traditional methods for mitigating chatter instability are called passive control which focuses on optimizing working spindle speeds and depths of cut. But they have inherent disadvantages in gaining highly efficient machining in milling processes. By contrast, the research in this paper is along the line of active control. Specifically, an adaptive algorithm is developed based on Fourier series analysis to deal with the so-called cutting force variation matrix which causes chatter instability. As a result, the chatter instability is remarkably mitigated. The performance improvement is illustrated by numerical simulation.