The splitting instability of a doubly-quantized vortex in the BEC-BCS crossover of a superfluid Fermi gas is investigated by means of a low-energy effective field theory. Our linear stability analysis and non-equilibrium numerical simulations reveal that the character of the instability drastically changes across the crossover. In the BEC-limit, the splitting of the vortex into two singly-quantized vortices occurs through the emission of phonons, while such an emission is completely absent in the BCS-limit. In the crossover-regime, the instability and phonon emission are enhanced, and the lifetime of a doubly-quantized vortex becomes minimal. The emitted phonon is amplified due to the rotational superradiance and can be observed as a spiraling pattern in the superfluid. We also investigate the influence of temperature, population imbalance, and three-dimensional effects.