Crownfire endangers fire fighters and can have severe ecological consequences. Prediction of fire behavior in tree crowns is essential to informed decisions in fire management. Current methods used in fire management do not address variability in crown fuels. New mechanistic physics-based fire models address convective heat transfer with computational fluid dynamics (CFD) and can be used to model fire in heterogeneous crown fuels. However, the potential impacts of variability in crown fuels on fire behavior have not yet been explored. In this study we describe a new model, FUEL3D, which incorporates the pipe model theory (PMT) and a simple 3D recursive branching approach to model the distribution of fuel within individual tree crowns. FUEL3D uses forest inventory data as inputs, and stochastically retains geometric variability observed in field data. We investigate the effects of crown fuel heterogeneity on fire behavior with a CFD fire model by simulating fire under a homogeneous tree crown and a heterogeneous tree crown modeled with FUEL3D, using two different levels of surface fire intensity. Model output is used to estimate the probability of tree mortality, linking fire behavior and fire effects at the scale of an individual tree. We discovered that variability within a tree crown altered the timing, magnitude and dynamics of how fire burned through the crown; effects varied with surface fire intensity. In the lower surface fire intensity case, the heterogeneous tree crown barely ignited and would likely survive, while the homogeneous tree had nearly 80% fuel consumption and an order of magnitude difference in total net radiative heat transfer. In the higher surface fire intensity case, both cases burned readily. Differences for the homogeneous tree between the two surface fire intensity cases were minimal but were dramatic for the heterogeneous tree. These results suggest that heterogeneity within the crown causes more conditional, threshold-like interactions with fire. We conclude with discussion of implications for fire behavior modeling and fire ecology.