This study investigates the wavy distribution of the cutting layer in an entire wellbore considering a dune mechanism. First, a fully transient two-layer model of cuttings transport is improved via two aspects: integrating the diffusion equation to calculate entrainment and deposition rates between two layers; and considering the buoyancy of cuttings motion in deviated sections. The new model is solved via a Stability Enhancing Two-Step (SETS) method. Next, an index is proposed, namely the ratio of the length of intervals with a height greater than 10% of the wellbore diameter to the entire wellbore length—to estimate the dynamic cleaning effect. Finally, the model is applied to an extended reach well, in which the wavy distribution of a cuttings bed as well as effects of buoyancy, mass exchange, and circulation stoppage are studied; further, the range of controllable parameter R (the time ratio of washing and pure drilling) is recommended.The results demonstrate that, in the iterative process of pure drilling and washing, the cuttings bed is no longer of equal height, but distributed in waves. The height of a cuttings bed decreases with an increase in R. This parameter should be greater than 0.5; otherwise, the gathered pile will severely threaten the subsequent drilling. When R reaches the upper limit of 1.2–2.5, the height of the cuttings bed is less than 10% the wellbore diameter, thus saving extra circulations. Moreover, the calculated bed height in the deviated section is lower when considering the buoyancy than when it is not. Thus, the middle section (inclination of 30°–60°) is not necessarily the most challenging area to clean if appropriate values for density and buoyancy of drilling fluids are considered. Furthermore, the cuttings bed slides downward after circulation is stopped, amassing on the lower side of the buildup section (70°–90°), which poses a significant risk of pipe sticking. The maximum stack height is nearly 1.2–2.5 times higher than that of the initial bed. With the increase of the inclination of the holding section, the stacking bed height increases rapidly when the angle is greater than 85°. The results serve as an essential guide to predict and control the tight spots more precisely for hole cleaning.