What you see is actually built on an entirely new 2-D/3-D animation system called Meander, which layers drawings on top of 3-D figures.
oh my god I thought it was made with pencil, but it was made with some 3D program. I was deluded, but I liked it so much, hahaha. So this video is very good, you can see how it was made. and search the original animation video, PAPERMAN, you’ll love it.