Background It is reported that lipid emulsion enriched in n-3 fatty acids (FAs) helps us to improve postoperative recovery for surgical patients with biliary tract disease. Its role for postoperative patients with obstructive jaundice is as yet unclear. The object of this study was to evaluate the safety and efficacy of n-3 fatty acid-based parenteral nutrition (PN) for patients with obstructive jaundice following surgical procedures. Methods Data were collected from patients with obstructive jaundice who received PN, including n-3 PUFA-enriched lipid emulsions and standard non-enriched lipid emulsions (e.g., soybean oil). We then calculated a propensity score, the probability of receiving different PN, by the propensity score matched (PSM) method. After matching, we compared isonitrogenous total PN with 20% Structolipid and 10% n-3 fatty acid (Omegaven, Fresenius-Kabi, Germany) (treatment group) to Structolipid alone (control group) for 5 days postoperatively, in the absence of enteral nutrition. Results Before the propensity score matching, there were 226 patients enrolled. After propensity score stratification, 108 cases remained, and all covariates were balanced. Among matched patients with PN, patients in the control group were at a higher risk for long-term jaundice recovery (12.9 +/- 8.5 VS 16.4 +/- 7.9 P = 0.029), lower velocity of reduction in jaundice (P = 0.045), and lower pre-albumin (P = 0.002). No significant difference as found in terms of comorbidities, white blood cell (WBC), albumin and other aspects. Conclusion PN with n-3 PUFA-enriched lipid emulsions was safe and effective in accelerating jaundice recovery for patients after surgical procedures.