Objective To investigate the clinic effect of minimally invasive surgery and craniotomy on treatment of hematencephalon. Methods 96 cases with hematencephalon in our hospital from February 2016 to February 2017 were selected and divided randomly into observation group and control group, 48 cases in each group. Control group was given craniotomy and observation group was given minimally invasive surgery. Treatment effect, complication rate, bleeding rate of the two groups were compared. Results Total effective rate of observation group and control group were 93.75%(45/48), 72.92%(35/48), the difference between groups was statistic significant (P<0.05), complication rate and bleeding rate of observation group 10.42%(5/48), 8.33%(4/48) were all significantly lower than control group 20.83%(10/48), 16.67%(8/48), the difference was statistic significant (P<0.05). Conclusion Minimally invasive surgery has better clinic effect on treatment of hematencephalon, complication rate and bleeding rate are lower, it is safe and reliable, and is wrothy of wide application.