A multiphysics analysis system for neutronics/thermomechanical/heat pipe thermal analysis of heat pipe–cooled micro reactors was developed using the PRAGMA code as the neutronics engine. PRAGMA, which was developed as a graphics processing unit (GPU)-based continuous-energy Monte Carlo code for power reactor applications, now has an extended geometry package to handle geometries with unstructured meshes generated by Coreform Cubit. The NVIDIA ray-tracing engine OptiX has been exploited for efficient neutron transport on unstructured mesh geometry. On the multiphysics side, the open-source computational fluid dynamics tool OpenFOAM and one-dimensional heat pipe analysis code ANLHTP have been adopted. The manager-worker system based on the message passing interface dynamic process management model enables efficient coupling of codes employing different parallelization schemes. With all the features, the multiphysics analysis of the 60-deg symmetrical sector model of the MegaPower three-dimensional core was performed for normal operation and heat pipe–failed conditions. The multiphysics coupling run time was about 2.5 h, in which the Monte Carlo simulation employing more than 10 billion histories was performed within half an hour on a single rack of computing nodes mounted with 24 NVIDIA Quadro GPUs. Accordingly, this demonstrates the soundness and robustness of the tightly coupled three-way multiphysics analysis system.