The objective of this study was to explore the effect of minimally invasive puncture drainage under unsupervised learning algorithm and conservative treatment on the prognosis of patients with cerebral hemorrhage. Fifty patients with cerebral hemorrhage were selected as the research objects. The CT images of patients were segmented by unsupervised learning algorithm, and the application value of unsupervised learning algorithm on CT images of patients with cerebral hemorrhage was evaluated. According to the treatment wishes of the patients themselves and their authorizers, they were divided into 30 patients with cerebral hemorrhage in the minimally invasive group and 20 patients with cerebral hemorrhage in the conservative group. The incidence rate of complications of cerebral hemorrhage, the length of hospitalization of the two groups, hematoma volume at admission, 3 days and 7 days after operation, and the hematoma dissipation rate on the 3rd and 7th day after operation were used as the evaluation index of therapeutic effect. MRS and ADL scores were used as prognostic indicators. The results show that K-means clustering algorithm has high quality and short time for CT image segmentation. The overall incidence rate of complications in minimally invasive group was 10%, lower than that in conservative group (25%) ( P < 0.05 ), and the length of hospitalization in minimally invasive group was longer than that in conservative group ( P < 0.05 ). The hematoma volume of minimally invasive group was 16.5 ± 2.4 mL on the 3rd day after operation, and that of conservative group was 27.4 ± 1.8 mL. There was significant difference between the two groups ( P < 0.05 ). In addition, CT showed that the hematoma reduction degree of minimally invasive group was higher than that of conservative group, and the hematoma dissipation rate was higher than that of conservative group on the 3rd and 7th day ( P < 0.05 ). The good MRS score in minimally invasive group was 3.15 times that in conservative group, and the good ADL score was 1.6 times that in conservative group, and there was significant difference in the total score between the two groups ( P < 0.05 ). Minimally invasive puncture drainage is better than conservative treatment in the clearance of hematoma, which is conducive to the recovery of neurological function and daily life of patients with cerebral hemorrhage and is of great help to the prognosis of patients.