Performing isothermal quenching heat treatment on austenitizing wires in a molten salt-bath can produce high-performance products. Meticulous regulation of the cooling process is essential for enhancing the performance of the wires. The research of this paper is based on the previous achievements of our research group. A three-dimension physical model is built to simulate the cooling process of the wires in the salt-bath. Through this model, this study first designs three new controlling flow hats and compares them with the original controlling flow hats from three perspectives: flow fields, entropy generations, and wire cooling rates, and finally selected the best performing hats. Subsequently, several groups of simulations are conducted under the boundary conditions of different salt capacities, temperatures and wires’ speeds to address the demand for increased capacity of the salt pump in the actual production. The main innovation of this article is to explore the synergistic effect of the salt temperature, capacity and wire speed on the optimal phase transition temperature, and determine the ideal salt temperature under the different salt capacities. In addition, the impact of the salt capacities on the wires’ thermo-uniformity and the range of phase transformation temperature is also studied. Finally, this article provides the molten salt-bath temperatures and wire speeds required to maintain the optimal phase transition temperature under three different salt capacities. This is of great significance for the renovation in actual production.