Compensation methods of beamlet deflections have been studied in a three dimensional (3D) beam analysis using OPERA-3d code for 1 MeV accelerator of the ITER neutral beam injector (NBI). The beamlet deflection is caused by i) magnetic field generated by permanent magnets embedded in the extraction grid (EXG) for electron suppression and ii) space charge repulsion between the beamlets and beam groups. Moreover, the beamlet deflection is caused due to electric field distortion formed by a grid support structure. In order to compensate the beamlet deflections due to i) and ii), an aperture offset of 0.6 mm was applied in the electron suppression grid (ESG) and a metal bar with 3 mm in thickness, so-called a kerb, was attached around the aperture area at the back side of the ESG, respectively. Detailed configuration of the compensation methods was also considered so as to suppress the beam spread due to the electric field distortion and to lower electric field concentrations at the edge of the kerb. For the beamlets near the grid support structure, the beamlet deflection due to the space charge repulsion could be negated due to the electric field distortion formed by the grid support structure.