A 3D dose reconstruction could detect many errors for IMRT plans, including delivery machine error and suboptimal treatment plans, as well as enhanced visualization of the beam deviation on volume target. In this study, we aim to develop an in-house software based on MATLAB to enable 3D dose calculation model based on 2D energy fluence data. A homogeneous virtual water phantom, which has a density of 1 g/cm3, was used to test the 3D reconstruction. We reconstructed the field sizes of 4×4, 10×10, and 15×15 cm2 from jaws only collimating to ensure that the algorithm agrees with the small field, standard field, and maximum opening field, in intensity-modulated radiotherapy (IMRT) treatment procedure. The evaluation was done for percentage depth doses (PDDs) and beam profiles. We found that the photon attenuation varies with increasing depth but remains the same after 10 cm depth of water. Moreover, it depends on the flattening filter and jaws design. The PDD of our algorithm was found to agree with the Monte Carlo (MC) simulation, with the average dose differences 1.07 ± 1.45%, 1.14 ± 3.49%, and 1.11 ± 1.52% for the field sizes of 4×4, 10×10, and 15×15 cm2, respectively. A large error was found in the build-up region, but still within 10%. The dose difference on beam profile was evaluated at zmax equals 1.6, 5, and 10 cm. The highest dose deviation of beam profile to MC simulation was found to be-35.5 ± 9.14% for the field size of 4×4 cm2 at zmax and decreases with increasing depth and field size of the photon beam.