Intensity-modulated radiotherapy and volumetric modulated arc therapy are modern radiation therapy technologies that can create the desired dose distribution by multileaf collimator movement and dose-rate control. However, the homogeneous dose delivery of small-field irradiation techniques shows disagreement with that of treatment planning system. The removal of the flattening filter by flattening filter free (FFF) beam irradiation increases dose conformity and further reduces treatment delivery time in radiosurgery. This study aims to investigate the dose distribution of FFF and flattened beams for small-field irradiation by using the 3D gel dosimeter. The N-isopropylacrylamide (NIPAM) polymer gel dosimeter was employed to record the 3D dose distribution. In addition, flattened and FFF beams were compared using the gamma evaluation technique. The use of an FFF accelerator resulted in excellent radiation treatments with short delivery times and low doses to normal tissues and organs. Results also showed that the passing rate increased with the decrease of field size (30 × 30, 20 × 20, and 10 × 10 mm2) at post-irradiation times of 24, 48, 72, and 96 h. The passing rates for each field size were retained at the same level when gamma criteria, namely, distance-to-agreement (DTA) = 3 mm/dose difference (DD) = 3%, were used. Nevertheless, the passing rates for each field size decreased slowly after 48 h when DTA = 2 mm/DD = 2%. The Wilcoxon signed-rank test was used to determine statistical difference with a significant level of p < 0.05. The passing rates of flattened and FFF beams showed no significant difference. The edge enhancement effect in the flattened beam was more evident than in the FFF beam. The 3D NIPAM gel dosimeter can be used for dose verification of small field for radiation therapy with high dose rate.