The objective of this study was to analyze the dynamics of nutrient balance, physiological biomarkers and comprehensive indexes associated with metabolism and function of organs in transition cows. Fourteen transition cows were used for this research. Dietary intake was recorded daily, and samples of the diet, venous blood and milk were collected for measurements. The balance values of net energy for lactation (NEL), metabolizable protein (MP), and metabolizable glucose (MG) were calculated, and regression analysis and calculation of comprehensive indexes were performed. Accordingly, the prepartum cows presented positive balances of NEL, MP, and MG, while severe negative balances were found during the postpartum period. Dynamic changes of energy metabolism, nutrient mobilization, liver function, anti-oxidative status and immune response, as indicated by blood biomarkers and modified comprehensive indexes, were out of sync with the calculated balance values, but they were closely related to the day relative to calving. Compared with the 21 d prepartum, the plasma concentrations of non-esterified fatty acids (NEFA) and β-hydroxybutyric acid (BHBA) were significantly increased around and after calving (P<0.05), and similar variation tendency was observed for most of other parameters. The occurrence of parturition and the initiation of lactation were more responsible for the negative balances of nutrients in transition dairy cows. Although negative balances of NEL, MP and MG were not observed using the assessment model, the nutritional strategies should be applied before calving, because metabolic adaptations had been validated during the prepartum period. In addition, it was plausible to conclude that the decline of hepatic metabolism, defense function and insulin sensitivity are critical causes of metabolic dysfunction.