CyberKnife is a robotic stereotactic body radiotherapy (SBRT) system that precisely delivers large radiation doses to a target. Tissue heterogeneity and shape can be problems. The treatment -planning system allows for use of the Monte Carlo (MC) or fundamental Ray Tracing (RyTc) algorithms for ultimate dose calculation. The MC is more accurate but consumes more computer resources and time. We compared radiation dose calculations for lung targets between the MC and RyTc algorithms. We placed a prosthetic marker at different thorax sites in a Rando phantom to compare the calculation results. The peripheral sites followed by the diaphragm showed the greatest significant differences in parameters for evaluating the treatment quality. For gross tumor volume dose, peripheral lung targets were the most critical for the calculation algorithm. The MC mean doses were lower than the RyTc mean doses and generally demonstrated better conformity. However, the deviation between conformal index (CI) and new CI at the peripheral location was large. The coverage differences between the RyTc and MC were most obvious at the peripheral lung site. The MC algorithm for radiation dose calculation in the lungs was indispensable in SBRT using CyberKnife for accurate dose evaluation, especially at the peripheral and diaphragm locations.