Background Myceliophthora thermophila has been engineered to be an important cell factory for malic acid production, however detail information on how carbon fluxes are distributed in the high production strain is still not clear. 13C-MFA (13C metabolic flux analysis) can help to understand cellular metabolic mechanisms and identify important targets for deciphering the carbon flux distribution and improving product synthesis. Here, we used 13C-MFA to study metabolic flux distribution of high malate production strain of M. thermophile for the first time. Results Higher glucose uptake and carbon dioxide release rate, together with lower oxygen consumption rate and biomass yield was found in malate high production strain M. thermophila JG207 compared to the wild strain. Corresponding to the above phenotypes, it is found that in JG207 both pentose phosphate pathway flux and oxidative phosphorylation flux decreased, while TCA downstream flux increased. Higher PPP flux in WT strain accompanied with higher energy state, and corresponding high ATP concentration inhibited glucose-6-phosphate isomerase activity. Several intermediates of reduced TCA pathway in JG207 were accumulated due to high reduction power state, which benefits the conversion of oxalate to malate. The reduced flux of oxidative phosphorylation is shown to be able to cover extra supply of NADH for high malate production. Conclusions This work revealed the intracellular metabolic fluxes distribution for the high malic acid production strain M. thermophile JG207 for the first time. The flux distribution results showed that higher NADH supply was of high importance for higher accumulation of malic acids, this may be guidance for further improvement of the productivity.