With the growing demand of multiprocessor system-on-chip (MPSoC) and 3D IC technology evolution, it is crucial to address power and thermal issues during system architecture design. Electronic system level (ESL) design is an acknowledged effective methodology to explore system design by virtual platforms. However, and to our best knowledge, current ESL virtual platforms only consider the performance and power issues. Therefore, we propose a run-time system thermal analysis framework for applications to an ESL virtual platform in order to analyze the thermal issue at an abstract level. In the experiment, the average estimation error of temperature was 3.18%, while the maximal estimation error was only 6.36% for ANSYS ICEPAK. The framework thus can help system designers explore power and thermal management at the early stages of IC development.