Molecular spin systems are characterized by a sizeable number of accessible energy levels that can be used to encode multi-level quantum logical units (qudits). Each molecular qudit can in principle replace several distinct two-level information carriers (qubits), thus reducing practical hardware requirements for quantum information processing and offering greater flexibility over conventional architectures. Here, a novel qudit-based platform for digital quantum simulations is designed by leveraging the large degree of chemical tunability and long coherence times of magnetic molecules. In fact, it is shown that molecular spin qudits provide an ideal setup to simulate the quantum dynamics of photon fields strongly interacting with matter. The basic unit of the proposed molecular quantum simulator could be realized by constructing a simple dimer of spin 1/2 and spin S ≥ 3/2 transition metal ions, solely controlled by microwave pulses. The spin S ion is exploited to encode the photon field, demonstrating how qudit logic may enable the digital simulation of a wide range of spin-boson models more efficiently compared to multi-qubit counterparts. The effectiveness of our proposal is demonstrated by numerical simulations using realistic molecular parameters for each of the two ions. The chemical prerequisites towards the synthesis of suitable proof-of-principle devices are also discussed. Overall, the result presented in this work strongly support the idea that chemistry can play a key role in the field of quantum technologies, providing a versatile route to build competitive quantum hardware.