Reducing underwater radiated noise from a ship is a critical issue for ensuring the survivability of the vessel. As high-speed signal processing and interlocking algorithms become more sophisticated, the heat intensity of shipboard equipment is increasing per unit volume. When designing shipboard equipment, it is necessary to consider the trade-off between heat dissipation and noise reduction. Following an analysis of the trade-offs, it was determined that the arrangement of Fan Ass'y A and B exhibited excellent noise and heat dissipation characteristics. Based on this, PWM control operating zones were derived. It was determined that the placement of Fan Ass'y A and B in the operating zone would increase the PWM duty cycle from 33% to 58% using a signal frequency of 25kHz band with guaranteed reliability. This would increase the noise by approximately 9dB(A) but reduce the internal board reference temperature by up to 15℃.