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Dynamical decoupling and Hamiltonian engineering are well-established techniques that have been used to control qubit systems. However, designing the corresponding methods for qudit systems has been challenging due to the lack of a Bloch sphere representation, more complex interactions, and additional control constraints. By identifying several general structures associated with such problems, we develop a formalism for the robust dynamical decoupling and Hamiltonian engineering of strongly interacting qudit systems. Our formalism significantly simplifies qudit pulse-sequence design while naturally incorporating robustness conditions necessary for experimental practicality. We experimentally demonstrate these techniques in a strongly interacting, disordered ensemble of spin-1 nitrogen-vacancy centers, achieving more than an order-of-magnitude improvement in coherence time over existing pulse sequences. We further describe how our techniques enable the engineering of exotic many-body phenomena such as quantum many-body scars, and open up new opportunities for quantum metrology with enhanced sensitivities. These results enable wide-reaching new applications for dynamical decoupling and Hamiltonian engineering in many-body physics and quantum metrology.