This experiment was conducted to investigate the effects of astragalus polysaccharides (APS) on serum metabolism of dairy cows under heat stress. Thirty healthy Holstein dairy cows were randomly divided into three groups (10 cows in each group). In the experimental group, 30 mL/d (Treatment I) and 50 mL/d (Treatment II) of APS injection were injected into the neck muscle respectively. Each stage was injected with APS for 4 days (8:00 a.m. every day) and stopped for 3 days. Serum hormone and antioxidant indexes of dairy cows were investigated. Through repeated measurement analysis of variance, the results have shown that cortisol (COR) (F = 6.982, p = 0.026), triiodothyronine (T3) (F = 10.005, p = 0.012) and thyroxine (T4) (F = 22.530, p = 0.002) at different time points were significantly different. COR showed a downward trend, T3 and T4 showed an upward trend. At each time point, different concentrations of APS have significant effects on COR (F = 30.298, p = 0.000 < 0.05), T3 (F = 18.122, p = 0.001), and T4 (F = 44.067, p = 0.000 < 0.05). However, there were no significant differences in serum insulin (INS), glucagon (GC) and heat shock protein 70 (HSP70) between different time points (p > 0.05) and at each time point (p > 0.05). Additionally, the results have also shown that there were also no significant differences in serum Superoxide dismutase (SOD), malondialdehyde (MDA) and lactate dehydrogenase (LDH) between different time points (p > 0.05) and at each time point (p > 0.05). However, the injection of APS had a significant impact on glutathione peroxidase (GSH-Px) (F = 9.421, p = 0.014) at different times, and showed a trend of rising first and then falling. At each time point, APS of different concentrations had no significant effect on GSH-Px (p > 0.05). Furthermore, we used gas chromatography–mass spectrometry (GC-MS) non-targeted metabolomics to determine the potential markers of APS for heat-stressed dairy cows. Twenty metabolites were identified as potential biomarkers for the diagnosis of APS in heat-stressed dairy cows. These substances are involved in protein digestion and absorption, glutathione metabolism, prolactin signaling pathway, aminoacyl-tRNA biosynthesis, pentose and glucuronate interconversions, and so on. Our findings suggest that APS have an effect on the serum hormones of heat-stressed dairy cows, and regulate the metabolism of heat-stressed dairy cows through glucose metabolism and amino acid metabolism pathways.