Large area multi-chip LED devices, such as chip-on-board (CoB) LEDs, require the combined use of chip-level multi-domain compact LED models (Spice-like compact models) and the proper description of distributed nature of the thermal environment (the CoB substrate and phosphor) of the LED chips. In this paper, we describe such a new numerical solver that was specifically developed for this purpose. For chip-level, the multi-domain compact modeling approach of the Delphi4LED project is used. This chip-level model is coupled to a finite difference scheme based numerical solver that is used to simulate the thermal phenomena in the substrate and in the phosphor (heat transfer and heat generation). Besides solving the 3D heat-conduction problem, this new numerical simulator also tracks the propagation and absorption of the blue light emitted by the LED chips, as well as the propagation and absorption of the longer wavelength light that is converted by the phosphor from blue. Heat generation in the phosphor, due to conversion loss (Stokes shift), is also modeled. To validate our proposed multi-domain model of the phosphor, dedicated phosphor and LED package samples with known resin—phosphor powder ratios and known geometry were created. These samples were partly used to identify the nature of the temperature dependence of phosphor-conversion efficiency and were also used as simple test cases to “calibrate” and test the new numerical solver. With the models developed, combined simulation of the LED chip and the CoB substrate + phosphor for a known CoB LED device is shown, and the simulation results are compared to measurement results.