Inactive ovaries (IO) and ovarian (follicular or luteal) cysts (FC or LC) are two common ovarian diseases leading to infertility in dairy cattle. Both disorders are associated with altered metabolites and hormones. There are currently no known effective biomarkers that can be used for early diagnosis of ovarian diseases. The purpose of this study was to identify the plasma biomarkers of ovarian diseases in Holstein dairy cows that facilitate an early diagnosis of the diseases and control its progression. The experiment was performed from 3 weeks postpartum and last for 7 weeks. Seventy-six multiparous Holstein cows (mean age, 4.36 years; weight, 635.63 kg) were divided into healthy control group (HC, n = 22), FC group (n = 18), LC group (n = 18) and IO group (n = 18) by rectal palpation or ultrasonography during the last 2 weeks before trial end. Blood was collected via tail vein for measurement of plasma energy metabolites, liver function indicators, minerals, and hormones at 3 and 8 weeks postpartum. Data were analyzed by Mann-Whitney U, Kruskal-Wallis, Spearman correlation, binary logistic regression analysis and receiver operating characteristic analysis, where applicable. At 8 weeks postpartum, FC cows had a more severe body condition score loss and these had greater levels of non-esterified fatty acids (NEFA) and estradiol, and lesser levels of alanine aminotransferase (ALT), progesterone and insulin-like growth factor 1 (IGF-1) levels than HC cows (P < 0.05). LC cows had a lower milk yield, higher NEFA and progesterone levels, and lower calcium, phosphorus and magnesium levels than HC cows (P < 0.05). IO cows had a lower body condition score, higher NEFA levels, and lower ALT, calcium, phosphorus, magnesium, estradiol, progesterone and IGF-1 levels than HC cows (P < 0.05). At 3 weeks postpartum, cows with ovarian diseases had greater (P < 0.05) concentrations of NEFA, and lesser concentrations of ALT, calcium, phosphorus and IGF-1 than HC cows. Early warning values for ovarian diseases were plasma NEFA concentrations >0.50 mmol/L, or calcium concentrations <2.02 mmol/L. Therefore, plasma NEFA and calcium could be used as early-warning indicators for ovarian diseases in dairy cows.