This meta-analysis aims to assess the effectiveness of virtual reality cognitive training (VRCT) and conventional computer-based cognitive training (CBCT) in five specific cognitive domains (i.e., global cognitive function (GCF), memory (Mem), executive function (EF), language (Lang) and visuospatial skills (VS)) of individuals with mild cognitive impairment. A total of 320 studies were yielded from five electronic databases. Eighteen randomized controlled trials met the PRISMA criteria, with 10 related to VRCT and 8 related to CBCT. A random-effect model was used in determining the main effect of cognitive training in five specific cognitive domains. VRCT provided the largest effect size on VS and Lang while the smallest on EF. CBCT provided the largest effect size on Mem and Lang while the smallest on EF. VRCT and CBCT generate an opposite effect on VS. VRCT outweighs CBCT in treatment effectiveness of GCF, EF, Lang and VS. More immersive and interactive experiences in VRCT may help individuals with MCI better engage in real-life experiences, which supports skill generalization and reduces external distractions. CBCT tends to improve Mem but no definite conclusions can be made. Further investigation with more stringent research design and specific protocol are required to reach consensus about the optimum intervention regime.