The Cooper-pair transistor (CPT), a small superconducting island enclosed between two Josephson weak links, is the atomic building block of various superconducting quantum circuits. Utilizing gate-tunable semiconductor channels as weak links, the energy scale associated with the Josephson tunneling can be changed with respect to the charging energy of the island, tuning the extent of its charge fluctuations. Here, we directly demonstrate this control by mapping the energy level structure of a CPT made of an indium arsenide nanowire with a superconducting aluminum shell. We extract the device parameters based on the exhaustive modeling of the quantum dynamics of the phase-biased nanowire CPT and directly measure the even-odd parity occupation ratio as a function of the device temperature, relevant for superconducting and prospective topological qubits.