The rapid growth of quantum technologies highlights the need for scalable models of computation that go beyond qubits and exploit the richer structure of Qudits. This paper introduces a novel and efficient approach for defining universal gate sets specifically designed for higher-dimensional Qudit systems ( \(N \ge 2\) ), addressing the limitations of traditional qubit-based approaches. We present a systematic methodology for constructing fundamental Qudit gates through the inherent structure of Qudit operators, providing a robust theoretical foundation for universal quantum computation with Qudits. Our rigorously proven universal and minimal gate set enables more efficient quantum circuit design. We demonstrate the construction of multidimensional extensions of controlled operations from these fundamental elements. To facilitate practical application, we provide a Python-based algorithm for decomposing arbitrary multi-Qudit operations, accompanied by detailed time- and space-complexity analyses. The framework is further validated through end-to-end implementations of Grover’s algorithm and QKD, comparing traditional gate constructions with circuits entirely synthesized from the proposed universal gate set (Code Repository: Minimal-Universal-Multi-Qudit-Gate-Sets ). These validations demonstrate not only the functional equivalence of the decomposed circuits, but also their direct relevance to the advancement of cryptographic protocols, paving the way for more efficient and secure Qudit-based quantum cryptography.