The　accurate　description　of　deformed　atomic　nuclei　by　orbital-free　density　functional　theory　has　been　a　longstanding　textbook　challenge,　due　to　the　difficulty　in　accounting　for　quantum　shell　effects.　Orbital-free　density　functional　theory　is,　in　principle,　capable　of　describing　all　nuclear　effects,　as　guaranteed　by　the　Hohenberg-Kohn　theorem.　However,　from　a　microscopic　perspective,　shell　and　deformation　effects　are　intrinsically　connected　to　single-orbital　structures,　posing　a　significant　challenge　for　orbital-free　approaches.　Here,　we　develop　a　machine-learning-based　orbital-free　density　functional　theory,　enabling　the　description　of　ground-state　properties　and　potential　energy　curves　for　both　spherical　16O　and　deformed　20Ne　nuclei.　To　our　knowledge,　this　is　the　inaugural　instance　where　a　fully　orbital-free　energy　density　functional　has　succeeded　in　taming　the　complex　nuclear　shell　and　deformation　effects.　It　demonstrates　that　the　orbital-free　approach,　rooted　directly　in　the　Hohenberg-Kohn　theorem,　is　not　only　a　theoretical　concept　but　also　a　practical　one　for　nuclear　systems.　©　The　Author(s)　2025.