Sunburn causes fruit browning and other physiological symptoms, reducing fruit production and quality. Therefore, we aimed to investigate the anatomical differences and abiotic stress responses in ‘Nichinan 1 gou’ satsuma mandarin (Citrus unshiu Marc.) according to the severity of sunburn damage (five grades: control, no sunburn; I to IV, increasing severity of sunburn). Additionally, the quality of sunburned and non-sunburned fruits was compared, and the sunburn-inducing temperature was estimated. Anatomical observations confirmed that with increased severity of symptoms, the damage to fruit rind surface and oil glands was increased. In the analysis of peel pigments, chlorophyll content in the rind gradually decreased compared with IV, whereas the carotenoid content gradually increased up to III. The flavonoid content in the peel and pulp was the highest in III. In the 1,1-diphenyl-2-picrylhydrazyl and 2,2′-azinobis (3-ethylbenzothiazoline-6-sulfonic acid) radical analyses, the IC50 (the concentration of compound at which the percentage of inhibition is 50%) value was the lowest in grade III in peel or IV in pulp, indicating a high free radical scavenging ability. The fruit quality analysis between sunburned and non-sunburned fruits showed differences in total soluble solid content, total acidity, firmness, coloration, and free sugar and organic acid contents, indicating a significant effect on fruit quality. In the heat tolerance tests on fruit rind in the laboratory and field, the damage was confirmed at temperatures above 47 °C.