Through systematical experiment design, the physical blowing agent (PBA) mass loss of bio-based polyurethane rigid foam (PURF) in the foaming process was measured and calculated in this study, and different eco-friendly PBA mass losses were measured quantitatively for the first time. The core of the proposed method is to add water to replace the difference, and this method has a high fault tolerance rate for different foaming forms of foams. The method was proved to be stable and reliable through the standard deviations $ {\sigma }_{1} $ and $ {\sigma }_{2} $ for $ {R}_{1} $ (ratio of the PBA mass loss to the material total mass except the PBA) and $ {R}_{2} $ (ratio of the PBA mass loss to the PBA mass in the material total mass) in parallel experiments. It can be used to measure and calculate the actual PBA mass loss in the foaming process of both bio-based and petroleum-based PURF. The results show that the PBA mass loss in PURF with different PBA systems is controlled by its initial mass content of PBA in PU materials $ \omega $. The main way for PBA to dissipate into the air is evaporation/escape along the upper surface of foam. This study further reveals the mechanism of PBA mass loss: the evaporation/escape of PBA along the upper surface of foam is a typical diffusion behavior. Its spread power comes from the difference between the chemical potential of PBA in the interface layer and that in the outside air. For a certain PURF system, $ {R}_{1} $ has approximately linear relationship with the initial mass content of PBA in PU materials $ \omega $, which can be expressed by the functional relationship $ {R}_{1}=k\omega $, where $ k $ is a variable related to PBA’s own attributes.