Radiation induced liver parenchymal changes after radiation therapy is depicted as a focal area of low signal intensity (FLSI) around the irradiated liver tumor on images of gadolinium ethoxybenzyl diethylenetriamine pentaacetic acid (Gd-EOB-DTPA)-enhanced magnetic resonance imaging (MRI). In 2014, we developed a real-time tumor-tracking function with two sets of fluoroscopic X-ray sources in the gantry and put it to use with spot-scanning proton beam therapy for moving tumors, we have called this real-time-image gated spot-scanning proton beam therapy (RGPT). The purpose of this study is to analyze the threshold dose (TD) for FLSI on Gd-EOB-DTPA-enhanced MRI after RGPT for hepatocellular carcinomas (HCC). We retrospectively reviewed patients with HCC treated by RGPT from December 2014 to October 2016 and followed this up with MRI using Gd-EOB-DTPA 3 months after the RGPT in our institution. We identified 10 patients with 11 lesions. Five patients had liver cirrhosis among the 10 patients. Before the RGPT, the median Child-Pugh score was 5 (range: 5-7) and nine patients were evaluated as Child -Pugh class A, with one as class B. The mean gross tumor volume was 33 ± 37 ml. Five patients received 76 Gy (relative biological effectiveness: RBE) in 20 fractions, three 72.6 Gy (RBE) in 22 fractions, and two patients with three lesions 66 Gy (RBE) in 10 fractions. We defined the FLSI as the low signal intensity area around the irradiated liver tumors on images in the hepatobiliary phase of Gd-EOB-DTPA-enhanced MRI 3 months after RGPT. The FLSI and the whole liver 3 months after RGPT were visually delineated. When we calculated the threshold dose (TD) for FLSI using a dose volume histogram, we adopted the non-FLSI liver volume (whole liver volume 3 months after RGPT minus the FLSI volume) to mitigate the impact of the shrinkage of the irradiated tumor and liver parenchyma within the FLSI. To analyze the TD among three treatment regimens, we used the equivalent dose in 2 Gy (RBE) fractions using a linear-quadratic model, assuming an α/β of 3. The mean liver volume before and after RGPT were 1278 ± 218 ml and 1218 ± 221 ml, respectively. The mean FLSI volume and non-FLSI liver volume were 143 ± 108 ml and 1061 ± 244 ml, respectively. The mean TD in 2Gy (RBE) fractions was 36.9 ± 11.0 Gy (RBE). The mean TD for patients with and without liver cirrhosis were 38.2 ± 10.8 Gy (RBE) and 34.9 ± 12.6 Gy (RBE), respectively (p = 0.673). The threshold dose for FLSI after RGPT on Gd-EOB-DTPA-enhanced MRI could be estimated in the RGPT planning for HCC. This would seem to be potentially useful in predicting liver damage before RGPT and prevent serious events in the following therapy.