Dietary intake is potentially associated with the onset of Crohn’s disease (CD), but evidence from epidemiological studies has remained unclear. This study aimed to evaluate the role of macronutrient intake in the development of CD. A systematic search was conducted in PubMed and Web of Science to identify all relevant studies, and the role of macronutrients in the development of CD was quantitatively assessed by dose–response meta-analysis. Four case-control studies (a total of 311 CD cases and 660 controls) and five prospective cohort studies (238,887 participants and 482 cases) were identified. The pooled relative risks (RR) for per 10 g increment/day were 0.991 (95% confidence interval (CI): 0.978–1.004) for total carbohydrate intake, 1.018 (95% CI: 0.969–1.069) for total fat intake, and 1.029 (95% CI: 0.955–1.109) for total protein intake. Fiber intake was inversely associated with CD risk (RR for per 10 g increment/day: 0.853, 95% CI: 0.762–0.955), but the association was influenced by study design and smoking adjustment. In subtypes, sucrose intake was positively related with CD risk (RR for per 10 g increment/day: 1.088, 95% CI: 1.020–1.160). Non-linear dose–response association was also found between fiber and sucrose intake and CD risk. In conclusion, this meta-analysis suggested a lack of association between total carbohydrate, fat or protein intake and the risk of CD, while high fiber intake might decrease the risk. In subtypes, high sucrose intake might increase the risk of CD.