Nanoscale friction on two-dimensional (2D) materials is closely associated with their mechanical, electronic and photonic properties, which can be modulated through changing thickness. Here, we investigated the thickness dependent friction on few-layer MoS2, WS2, and WSe2 using atomic force microscope at ambient condition and found two different behavior. When a sharp tip was used, the regular behavior of decreasing friction with increasing thickness was reproduced. However, when a pre-worn and flat-ended tip was used, we observed an abnormal trend: on WS2 and WSe2, friction increased monotonically with thickness, while for MoS2, friction decreased from monolayer to bilayer and then subsequently increased with thickness. As suggested by the density functional theory calculation, we hypothesize that the overall frictional behavior is a competition between the puckering effect and the intrinsic energy corrugation within the compressive region. By varying the relative strength of the puckering effect via changing the tip shape, the dependence of friction on sample thickness can be tuned. Our results also suggest a potential means to measure intrinsic frictional properties of 2D materials with minimum impact from puckering.