It is known that microtrauma exists in the thigh muscles after long-distance running such as the half-marathon. Moreover, training characteristics of long-distance runners may influence the specificity of the distribution of muscle fiber types in the thigh and affect muscle responses to lipid metabolism. However, the specific changes in microtrauma and intramuscular lipid in thigh muscles after a half-marathon are unknown. A cohort of 20 healthy recreational marathon runners was recruited to complete a half-marathon. MRI T2 mapping and 6-echo q-Dixon sequences were employed at baseline (P1), 2-3h after running (P2), and 1day after running (P3). Inflammatory markers (the T2 values) and intramuscular fat fraction (the proton density fat fraction, PDFF) were measured in thigh muscles to detect microtrauma and intramuscular lipid changes, respectively. One-way analysis of variance showed significant time effects for T2 values and PDFF. Post hoc analysis of the 14 datasets collected at three time points revealed significantly higher T2 values in all thigh muscles after running (all p<0.05). Significant differences in T2 values persisted for all thigh muscles at P3 compared to P1 (all p<0.05). The PDFF of the vastus lateralis and vastus medialis was significantly decreased at P2 compared to P1 (p<0.05). No significant differences in PDFF were observed for the thigh muscles at P3 compared to P1. The manifestations of inflammation edema and intramuscular lipid investigated through MRI may offer valuable insights for recreational marathon runners regarding the lower limb movement characteristics during half-marathon running.