We show that molecular spin qudits provide an ideal platform to simulate the quantum dynamics of photon fields strongly interacting with matter. The basic unit of the proposed molecular quantum simulator can be realized by a simple dimer of a spin 1/2 and a spin $S$ transition metal ion, solely controlled by microwave pulses. The spin $S$ ion is exploited to encode the photon field in a flexible architecture, which enables the digital simulation of a wide range of spin-boson models much more efficiently than by using a multi-qubit register. The effectiveness of our proposal is demonstrated by numerical simulations using realistic molecular parameters, whose prerequisites delineating possible chemical approaches are also discussed.