This study aims to compare the prostate cancer detection rate between magnetic resonance imaging (MRI)-transrectal ultrasound (TRUS) cognitive fusion targeted biopsy and systematic biopsy. A total of 614 patients who underwent transrectal prostate biopsy during 2016-2018 with multiparametric magnetic resonance imaging (mpMRI) were included. All patients with a PI-RADS V2 score ≥ 3 accepted both targeted biopsy and systematic biopsy, and those with a PI-RADS V2 score ≤ 2 only accepted systematic biopsy. Overall prostate cancer detection rate between the two biopsies was compared. MRI-TRUS cognitive fusion targeted biopsy identified 342 cases (75.7%) of prostate cancer while systematic biopsy identified 358 cases (79.2%). There was no significant difference in the detection rate between the two groups (χ2 = 1.621, P = 0.203). Targeted biopsy had significant fewer biopsy cores compared with systematic biopsy, reducing (9.3 ± 0.11) cores (P < 0.001) in average. Targeted biopsy had about 10.8% (P < 0.001) more tumor tissues in positive cores compared with systematic biopsy. The results show that both MRI-TRUS cognitive fusion targeted biopsy and systematic biopsy have good detection rate on prostate cancer. Cognitive targeted biopsy may reduce biopsy cores and provide more tumor tissues in positive cores.