Purpose: The metabolites phosphocreatine (PCr), adenosine triphosphate (ATP), and in-organic phosphate (Pi) are biochemically coupled. Their pool sizes, assessed by their magnetization ratios, have been extensively studied and reflect bioenergetics status in vivo. However, most such studies have ignored chemical exchange and T 1 relaxation effects. In this work, we aimed to extend the T nom 1 method to simultaneously quantify the reaction rate constants as well as phosphorus metabolite pool size ratios under partially relaxed conditions. Materials and Methods: Modified Bloch-McConnell equations were used to simulate the effects of chemical exchanges on T 1 relaxation times and magnetization ratios among PCr, c-ATP, and Pi. The T nom 1 method with iteration approach was used to measure both reaction constants and metabolite pool size ratios. To validate our method, in vivo data from rat brains (N 5 8) at 9.4 Tesla were acquired under two conditions, i.e., approximately full relaxation (TR 5 9 s) and partial relaxation (TR 5 3 s). We compared metabolite pool size ratios and reaction constants before and after correcting the chemical exchange and T 1 relaxation effects. Results: There were significant errors in underestimation of PCr/cATP by 12 % (P 5 0.03) and overestimation of ATP/Pi ratios by 14 % (P 5 0.04) when not considering chemical exchange effects. These errors were minimized using our iteration approach, resulting in no significant differences (PCr/cATP, P 5 0.47; ATP/Pi, P 5 0.81) in metabolite pool size ratios and reaction constants between the two measurements (i.e., short versus long TR conditions). Conclusion: Our method can facilitate broad biomedical applications of 31 P magnetization saturation transfer spectroscopy, requiring high temporal and/or spatial resolution for assessment of altered bioenergetics. P hosphorus magnetic resonance spectroscopy ( 31 P-MRS) provides insight into bioenergetic impairment and mitochondrial dysfunction in vivo under various physiological and pathological conditions. 1-5 Major phosphorus-containing metabolites related to bioenergetics detected by in vivo 31 P-MRS include phosphocreatine (PCr), inorganic phosphate (Pi), and adenosine triphosphate (ATP) with the a-, b-, and c-resonances. These metabolites compose a chemical exchange network (PCr$ATP$Pi) catalyzed by the enzymes creatine kinase (CK) and ATP synthase (ATPase). These chemical reactions are crucial for regulating ATP metabolism and maintaining normal ATP functionality. The phosphorus metabolite levels or pool sizes assessed by their magnetization ratios such as PCr to c-ATP (PCr/c-ATP), c-ATP to Pi (c-ATP/Pi), and PCr to Pi (PCr/Pi) have been extensively studied in various disease states in vivo, for instance in the brain, 6-8 heart, 9,10 and muscle. 2,11 For measuring phosphorus-containing metabolite levels using a conventional MRS approach, Ernst and Anderson 12 suggested that large improvements in signal-to-noise ratio (SNR) per unit sampling time could be achieved by the use of short inter-pulse del...