Background The impact of p-cresyl sulfate (PCS) and indoxyl sulfate (IS) on the prognosis of patients with uremia remains controversial. We performed a prospective study on peritoneal dialysis (PD) to investigate the relationship between PCS or IS levels with clinical outcomes. Methods This prospective cohort study investigated the association of serum PCS and IS with clinical outcomes in patients undertaking PD. We performed a correlations analysis to explore the influencing factors of PCS an IS. Meta-analysis was conducted to objectively evaluate the prognostic effects of PCS and IS on different stages of CKD patients. Results A total of 127 patients were enrolled consecutively and followed with an average period of 51.3 months. Multivariate Cox regression showed that serum total PCS not only contributed to the occurrence of PD failure event (HR: 1.05, 95% CI = 1.02 to 1.07, p < 0.001), but also increased the risk of cardiovascular event (HR: 1.08, 95% CI = 1.04 to 1.13, p < 0.001) and PD-associated peritonitis (HR: 1.04, 95% CI = 1.02 to 1.08, p = 0.001). Dividing the total PCS level by 18.99 mg/L, which was calculated from the best cutoff value of the ROC curve, patients with total PCS higher than 18.99 mg/L had worse prognosis. Meta-analysis confirmed its value in cardiovascular event in PD. Conclusion The serum total PCS concentration was a detrimental factor for higher PD failure event, cardiovascular event, and PD-associated peritonitis. It could be used as an innovative marker in predicting poor clinical outcome in PD.