This study aimed to assess the diagnostic values of peptidoglycan (PGN), lipopolysaccharide (LPS) and (1,3)-Beta-D-Glucan (BDG) in patients with suspected bloodstream infection. We collected 493 heparin anticoagulant samples from patients undergoing blood culture in Peking Union Medical College Hospital from November 2020 to March 2021. The PGN, LPS, and BDG in the plasma were detected using an automatic enzyme labeling analyzer, GLP-F300. The diagnostic efficacy for PGN, LPS, and BDG were assessed by calculating the sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV). This study validated that not only common bacteria and fungi, but also some rare bacteria and fungi, could be detected by testing the PGN, LPS, and BDG, in the plasma. The sensitivity, specificity, and total coincidence rate were 83.3%, 95.6%, and 94.5% for PGN; 77.9%, 95.1%, and 92.1% for LPS; and 83.8%, 96.9%, and 95.9% for BDG, respectively, which were consistent with the clinical diagnosis. The positive rates for PGN, LPS, and BDG and the multi-marker detection approach for PGN, LPS, and BDG individually were 11.16%, 17.65%, and 9.13%, and 32.86% significantly higher than that of the blood culture (p < 0.05). The AUC values for PGN, LPS, and BDG were 0.881 (0.814–0.948), 0.871 (0.816–0.925), and 0.897 (0.825–0.969), separately, which were higher than that of C-reactive protein (0.594 [0.530–0.659]) and procalcitonin (0.648 [0.587–0.708]). Plasma PGN, LPS, and BDG performs well in the early diagnosis of bloodstream infections caused by Gram-positive and Gram-negative bacterial and fungal pathogens.