Machining parameters and spindle radial runout have great influence on the micro-ball-end cutter deflection in the micro-end-milling process. In this study, a 3D (three-dimensional) thermal-mechanical FEM (finite element method) model of micro-milling with non-rigid cutter is built to study how radial runout, cutting depth, feed and spindle speed influence the cutter deflection when feed has the same direction with the spindle radial runout. Cutter deflection under different groove lengths, cutting depths, feeds and spindle speeds is investigated, which shows that cutter deflection increases with spindle radial runout significantly. The largest deflections with runout of 2μm are 3.26μm, 3.26μm, 4.71μm and 4.52μm respectively under the adopted machining conditions, while the largest deflections without runout are 1.85μm, 1.85μm, 2.26μm and 3.79μm respectively. It is also shown that the runout effect increases with groove length, cutting depth, while it decreases with feed.