Background and objective Branch atheromatous disease (BAD) is highly susceptible to early neurological deterioration (END), resulting in a poor prognosis for patients. However, there is no reliable serum biomarker for BAD. The aim of this study is to investigate the correlation between CT perfusion imaging combined with serum soluble urokinase plasminogen activator receptor (suPAR) and Mac-2 binding protein (Mac-2BP) with END and poor prognosis in patients with BAD. Methods Between June 2019 and March 2024, We prospectively recruited eligible BAD patients admitted to the neurology department. END is defined as an increase of ≥ 2 points in the total score of the National Institutes of Health Stroke Scale (NIHSS) or an increase of ≥ 1 point in the exercise score within 72 hours after admission; Using the modified Rankin scale (mRS) to evaluate the clinical outcomes of patients at 90 days, poor outcomes were defined as mRS scores ≥ 3 points at 90 days after onset; Define cerebral perfusion damage based on CTP imaging parameters. Compare suPAR and Mac-2BP levels between END and non END patients, as well as patients with different clinical outcomes. Use multivariate logistic regression to analyze independent influencing factors of END in patients with BAD, and use receiver operation characteristic curve (ROC) to analyze the accuracy of serum suPAR and Mac-2BP in predicting END and poor outcomes. Results A total of 176 patients with BAD were included, of which 90 had significant cerebral perfusion damage, 42 developed END, and 47 had poor outcomes at 90 days of onset. Multivariate logistic regression analysis showed that suPAR (OR 0.706, 95% CI 0.573 ~ 0.868)、Mac-2BP (OR 0.674,95% CI 0.486 ~ 0.935),、Cerebral perfusion impairment (OR 6.083, 95% CI 1.318 ~ 28.080)、deep WMHs (OR 1.967, 95% CI 0.884 ~ 2.751) and deep CMBs (OR 2.249, 95% CI 1.113 ~ 3.126) are independent risk factors for END in patients with BAD; suPAR(OR 6.702,95% CI 2.776 ~ 16.182)、Mac-2BP (OR 1.707, 95% CI 1.132 ~ 2.576)、NIHSS score at END (OR 0.529, 95% CI 0.339 ~ 0.824)、END (OR 1.286, 95% CI 1.016 ~ 1.628)、Cerebral perfusion impairment (OR 12.873, 95% CI 2.744 ~ 60.385) and basal ganglia EPVS (OR 1.509, 95% CI 1.019 ~ 2.233) are independent risk factors for poor outcomes. The ROC curve shows that the AUC of suPAR and Mac-2BP combined for detecting END is 0.8844 (95% CI: 0.822–0.947), with sensitivity and specificity of 76.2% and 85.1%, respectively; The AUC of the combined detection of two indicators for poor outcomes was 0.8742 (95% CI: 0.810 ~ 0.938), with a sensitivity and specificity of 74.5% and 83.9%, respectively. Conclusions Among BAD patients, Cerebral perfusion impairment, suPAR, and Mac-2BP are independent risk factors for poor outcome at END and 90 days. Combined detection can help evaluate the patient's condition and predict prognosis.