The study of blood flow in obstructed arteries is a significant focus in computational fluid dynamics, particularly in the field of biomedicine. The primary objective of this research is to investigate the impact of pulsating blood velocity on heat transfer within biological systems, with a specific focus on blood flow in obstructed arteries. To achieve this goal, a comprehensive 3D model representing a straight, constricted blood vessel has been developed. This model incorporates periodic, unsteady, Newtonian blood flow along with the presence of gold and silver nanoparticles. Leveraging the Finite Element Method (FEM), the Navier-Stokes and energy equations have been rigorously solved. Through the investigation, it is aim to shed light on how alterations in the pulsation rate and the volume fraction of nanoparticles influence both temperature distribution and velocity profiles within the system. The present study findings unequivocally highlight that the behavior of pulsatile nanofluid flow significantly impacts the velocity field and heat transfer performance. However, it is imperative to note that the extent of this influence varies depending on the specific volume fractions involved. Specifically, higher volume fractions of nanofluids correlate with elevated velocities at the center of the vessel and decreased velocities near the vessel walls. This pattern also extends to the temperature distribution and heat flux within the vessel, further underscoring the paramount importance of pulsatile flow dynamics in biomedicine and computational fluid dynamics research. Besides, results revealed that the presence of occlusion significantly affects the heat transfer and fluid flow.