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This video uses almost no 3d at all from what I’ve seen! They use a mix of some regular hand-animation for some secondary motions and a feature in Adobe After Effects called Puppet Warp which basically creates a tessellated geometric mesh around an image(usually transparent) and applies the image to this new mesh as a texture. This tessellated geometry is then what actually gets moved around and animated and “rigged”. There are options to set the density of the tessellation which can help with certain errors in granularity(tight bends or jagged deformations, etc).

Each “pin” is animatable with keyframes just like any other key-frame-able point in After Effects and supports expressions and such. The music video makes careful sure that strands of hair and frilly cloth are moving somewhat or that certain limbs are moving at their joints(when miku is getting her hair brushed) and at some points to get an entire character to walk(the silhouette in the intro).

Making assets for a workflow involving puppet-warping like that requires the layers of the animating artwork be preserved so that you can get specific parts of a “rig” to move independently of another(hair moving in front of a face, clothes moving over skin, etc).

I’ve used it here and there when making videos and even used it for pixel art related stuff!