In this paper, a novel distributed unified controller is designed to solve the problems of unbalanced State of Charge (SoC), unreasonable load current sharing, and unstable DC bus voltage for parallel battery storage systems (BSSs) in DC shipboard microgrid (DC-SMG). Different from the droop-based secondary controller, the designed distributed unified controller is a droop-free primary controller, which can incorporate SoC balancing, current sharing, and voltage regulation functions in the primary control layer. On this basis, each BSS uses an improved dynamic diffusion algorithm (DDA) to iteratively estimate the average information, and completes information exchange by a neighbor-to-neighbor communication network. Furthermore, the small-signal stability, large-signal stability, and global steady-state performance of the system is investigated using eigenvalue analysis, mixed potential theory (MPT), and matrix theory, respectively. Finally, the Matlab/Simulink simulation model and the StarSim HIL experimental platform for DC-SMG are built. The results show that the designed distributed unified controller can simultaneously achieve dynamic SoC balancing, proportional load current sharing, and smooth average bus voltage regulation, and has a faster SoC convergence speed and more stable control effect than the state-of-the-art methods.