The changes of microconfiguration and dynamic changes of monoamines, 5-hydroxytryptamine (5-HT), norepinephrine (NE) and dopamine(DA), in the rat endbrain after exhaustive swimming were observed in order to provide objective reference for evaluation of exercise central fatigue. Thirty-six male SD rates were divided randomly into 4 groups: group control (G1); group immediate after exhaustive swimming (G2); group 24 hours after exhaustive swimming (G3) and group 48 hours after exhaustive swimming (G4), 9 in each group. After adaptive swimming for 4 days, rats in G2, G3 and G4 took loaded swimming in ratio of 5 g for every 100g body weight (5%) till exhaustion. After decapitation, the endbrains of the rats in each group were taken for ordinary electron microscopic observation of change of microcofiguration and measurement of contents of 5-HT, NE and DA by fluorometric photometer. The ultrastructure of the endbrain cortex in G2 had apparent changes. In G3, improvement of ultrastructure of microcirculation in endbrain were observed; In G4, structure of microcirculation almost recovered to normal level. The level of 5-HT and NE in the endbrain of exhaustive swimming rat increased significantly, up to the highest in G3 (24h). It was therefore demonstrated that the configuration change of microcirculation and change of 5-HT and NE contents in rat endbrain after exhaustive exercise were synchronous and that the recovery of the configuration change of microcirculation was faster than change of 5-HT and NE contents, the ultrastructure change of microcirculation being reversible. These results indicate that the improvement of microcirculation in endbrain can help promote recovery of sporting central fatigue.