To develop and validate a 3D simulation model to calculate laser ablation (LA) zone size and estimate the volume of treated tissue for thyroid applications, a model was developed, taking into account dynamic optical and thermal properties of tissue change. For validation, ten Yorkshire swines were equally divided into two cohorts and underwent thyroid LA at 3 W/1,400 J and 3 W/1,800 J respectively with a 1064-nm multi-source laser (Echolaser X4 with Orblaze technology; ElEn SpA, Calenzano, Italy). The dataset was analyzed employing key statistical measures such as mean and standard deviation (SD). Model simulation data were compared with animal gross histology. Experimental data for longitudinal length, width (transverse length), ablation volume and sphericity were 11.0 mm, 10.0 mm, 0.6 mL and 0.91, respectively at 1,400 J and 14.6 mm, 12.4 mm, 1.12 mL and 0.83, respectively at 1,800 J. Gross histology data showed excellent reproducibility of the ablation zone among same laser settings; for both 1,400 J and 1,800 J, the SD of the in vivo parameters was ≤ 0.7 mm, except for width at 1,800 J, for which the SD was 1.1 mm. Simulated data for longitudinal length, width, ablation volume and sphericity were 11.6 mm, 10.0 mm, 0.62 mL and 0.88, respectively at 1,400 J and 14.2 mm, 12.0 mm, 1.06 mL and 0.84, respectively at 1,800 J. Experimental data for ablation volume, sphericity coefficient, and longitudinal and transverse lengths of thermal damaged area showed good agreement with the simulation data. Simulation datasets were successfully incorporated into proprietary planning software (Echolaser Smart Interface, Elesta SpA, Calenzano, Italy) to provide guidance for LA of papillary thyroid microcarcinomas. Our mathematical model showed good predictability of coagulative necrosis when compared with data from in vivo animal experiments.