Background: Nowadays, the anterior cruciate ligament (ACL) injury has been one of the most common diseases of the knee joint. The relationships between the ACL injury and the anatomical structures are still controversial. This study aimed to identify the anatomical risk factors of ACL injury by magnetic resonance imaging (MRI) of the knee. Methods: This was a retrospective study of 125 patients undergoing primary ACL reconstruction between July 2013 and May 2017. Another 125 patients without any organic knee joint injury were served as controls. The shape of intercondylar notch, the intercondylar notch width index, the intercondylar notch height index, the α angle, the β angle, and the medial and lateral tibial plateau slope were measured with MRI and compared. The data were compared by binary logistic regression to find the risk factors. Results: The two groups differed in the proportion of male patients (70.4% vs. 52.0%, χ2 = 8.911, P = 0.003), but gender was excluded as a risk factor for ACL injury with regression analysis (odds ratio = 1.476, 95% confidence interval [ CI]: 0.689–3.160, P = 0.317). The injured group was found to have a smaller notch width index (95% CI = 7.960E-23–2.154E-9, P < 0.001), a larger β angle (95% CI = 1.311–1.785, P < 0.001), and a larger lateral tibial plateau slope (95% CI = 1.201–1.683, P < 0.001). The cutoff values of notch width index, β angle, and the lateral tibial plateau slope were 0.252, 38.5°, and 7.5°, respectively. Conclusions: In this study, a narrow intercondylar notch (intercondylar notch width index <0.252), a larger lateral tibial slope (>7.5°), and larger β angle (>38.5°) might be the factors associated with ACL injury. Trial Registration: ChiCTR-RRC-17014116;http://www.chictr.org.cn/showproj.aspx?proj=24119.