Crop magnesium (Mg) deficiency is widespread in global agriculture, but limited assessment is available on how crop yield could respond to Mg fertilization at national or regional scale. This meta-analysis from 196 paired datasets evaluated the different yield responses of 49 crop species under Mg fertilization at the southern and northern region of China where 50% soils were Mg-deficient. The results showed that under Mg fertilization the crop yields were averagely increased by 19.2%, 11.3% and 16.6% in southern China, northern China and the whole country, respectively. Meanwhile, significantly greater yield increment of crop types under Mg fertilization ranked as vegetables (20.1%) ≈ fruits (19.6%) >cereals (6.5%). In conclusion, Mg fertilization is recommended to enhance yield and quality of fruit and vegetable crops in subtropical and tropical China and other similar countries.