Magnetic impurities have a dramatic effect on superconductivity by breaking the time-reversal symmetry and inducing so-called Yu-Shiba-Rusinov (YSR) low energy bound states within the superconducting gap. The spatial extent of YSR states is greatly enhanced in two-dimensional (2D) systems, which should facilitate the formation of coupled states. Here, we observe YSR states on single cobalt phthalocyanine (CoPC) molecules on a 2D superconductor NbSe2 using low-temperature scanning tunneling microscopy (STM) and spectroscopy. We use STM lateral manipulation to create controlled CoPc dimers and demonstrate the formation of coupled YSR states. The experimental results are corroborated by theoretical analysis of the coupled states in lattice and continuum models.