Phase-change materials (PCMs) are commonly employed in building service equipment to regulate indoor temperatures and reduce energy consumption. This study conducted multi-scale finite element modeling to analyze the steady-state and dynamic thermal behavior of a hydronic radiant floor heating system integrated with macro-encapsulated PCMs. It predicted performance values for hydronic floor heating with and without macro-encapsulated PCMs. The study assessed the impact of the PCM volume fraction, heating water temperature, capsule thermal conductivity, and shape on the thermal performance of hydronic floor heating through various finite element models. The predictive capability of the finite element model was validated using experimental data, showing good agreement. Although the inclusion of PCMs lowered the floor temperature, it improved temperature distribution and retained heat when the system was inactive. The PCM volume fraction significantly influenced the performance of the hydronic floor. However, the shape of the macro-encapsulated PCM and thermal conductivity of the shell had minimal effects in the studied case. For instance, increasing the thermal conductivity of the shell of the PCM capsule fifty times from 0.3 to 15 W m−1 K−1 resulted in an increase in surface temperature by 1.2 °C.