The cores of massive neutron stars offer a unique environment for the nuclear matter at intermediate density in the universe. The global characteristics of a neutron star, as well as the gravitational waves emitted from the mergers of two neutron stars, offer valuable insights into dense nuclear matter. In this paper, we comprehensively investigate the effect of the potential hadron-quark transition on the properties of neutron stars and the signals of the gravitational waves stemming from the merger of binary neutron stars, including waveforms, frequency evolutions as well as the spectrum curves, utilizing the equations of state constructed from the Maxwell ansatz, Gibbs ansatz and, the crossover scenario. We explicitly construct the equations of state in such a way that they converge at low and high densities therefore the differences are only from the scenarios of the transitions and the locations—or the parameters in the equation of state. Using such constructed equations of state, we simulate the signals of the gravitational wave (GW) and analyze their differences due to locations of the transition, the scenarios of the transition, and the masses of the component stars. We find that (1) in both the Maxwell ansatz and Gibbs ansatz, GW signals are sensitive to the location and the latent heat of the phase transition, (2) in the post-merger phase, the frequency of GW increases with the evolution in Maxwell type transition but is stable in the other two types of transitions and, (3) the amount of radiated energy is the biggest in Gibbs construction (GC) type transition and the smallest in the crossover construction (CC) type transition. By combining our findings with the expected detection of gravitational waves around (2–4) kHz from binary neutron star mergers and their associated electromagnetic signals, we expect to uncover some key characteristics of dense nuclear matter.