Water is a weakly compressible fluid medium. Due to its low compressibility, it is usually assumed that water is an incompressible fluid. However, if there are high-pressure pulse waves in water, the compressibility of the water medium needs to be considered. Typical engineering applications include water hammer protection and pulse fracturing, both of which involve the problem of discontinuous pulse waves. Traditional calculation and simulation often use first-order or second-order precision finite difference methods, such as the MacCormark method. However, these methods have serious numerical dissipation or numerical dispersion, which hinders the accurate evaluation of the pulse peak pressure. In view of this, starting from the weakly compressible Navier–Stokes (N-S) equation, this paper establishes the control equations in the form of flux, derives the expressions of eigenvalues, eigenvectors, and flux vectors, and gives a new flux vector splitting (FVS) formula by considering the water equation of state. On this basis, the above flux vector formula is solved using the fifth-order weighted essentially non-oscillatory (WENO) method. Finally, the proposed FVS formula is verified by combining the typical engineering examples of water hammer and pulse fracturing. Compared with the traditional methods, it is proved that the FVS formula proposed in this paper is reliable and robust. As far as we know, the original work in this paper extends the flux vector splitting method commonly used in aerodynamics to hydrodynamics, and the developed model equation and method are expected to play a positive role in the simulation field of water hammer protection, pulse fracturing, and underwater explosion.