Purpose: Internal temperature is a significant factor for medical diagnosis. There are several thermometric methods, including IR, MRI, and active ultrasonic thermometry, which have limitations for clinical applications. The new method in this field called Passive Acoustic Thermometry (PAT), which enhanced some of this limitation. PAT is a safe method for internal temperature estimation that works based on acoustic radiation of materials with a specific temperature. Several experimental studies have been carried out so far in the field of PAT. While, to the best of our knowledge, there is no simulation-based research for nonhomogeneous materials reported yet. In this article (for the first time) we proposed a simulation framework for evaluating the PAT methodologies in nonhomogeneous materials; also we proposed a new formulation for temperature estimation in PAT algorithm. Materials and Methods: This framework supports the generation of acoustic radiation, signal processing, parameter estimation, and temperature reconstruction processes. At the moment the proposed framework estimates the temperature in the frequency domain and uses the frequency spectrum of the acquired ultrasound signals captured by a single transducer. Using the proposed framework, we tried to implement the previously practical experiments and the results of the simulation are consistent with those of the practical experiments. Also, we proposed the formulation that improves the error of temperature estimation. Results: We study 6 scenarios, including 2 environments with a target at 3 different temperatures. The average error of the proposed formulation in two different nonhomogeneous materials for three different temperatures is less than 0.25°C. Conclusion: The results show that the proposed formulation is the best estimation in the formula that has been introduced until now and compare with the previous study the accuracy is enhanced 54% (from 0.79 to 0.36 deg.). Therefore, the proposed formula enhanced PAT accuracy for temperature estimation. Also, the results show that it is possible to use this framework to evaluate the PAT in different scenarios. Therefore, this method enhances the possibility of examination of different conditions and algorithms. It also reduces the cost of practical experiment.