Sustainable intensification of agriculture is needed to meet higher future food demands while mitigating agriculture’s ecological footprint. Intercropping is a strategy for increasing agricultural productivity per unit land that is based on ecological mechanisms for improved resource capture. No quantitative synthesis has been made on the effect of intercrop system properties and species trait combinations on intercrop productivity. Here we use meta-analysis of the intercropping literature to study how the productivity of mixed systems is affected by intercrop system design and species traits. We focus on the effects of temporal niche differentiation between species, intercropping pattern, relative densities, the use of C3 and C4 species and the rate of nitrogen fertilizer. Land equivalent ratio (LER) is used as index for assessing the relative productivity of a mixed system as compared to sole crops. Average LER was 1.22 ± 0.02, and no differences in LER were found between the 50 most highly cited studies and a random sample from the literature, indicating that high LERs in highly cited papers are representative of the entire literature. Temporal niche differentiation contributed substantially to high LER in systems combining a C3 and C4 species, but not in systems based on C3 species mixtures. The amount of N fertilizer interacted positively with the effect of temporal niche differentiation on LER. The intercropping literature is dominated by studies on cereal/legume mixtures. However, the few studies on C3 cereal/C4 cereal mixtures indicate these mixtures have high LER. Substantial improvements in land use efficiency in agriculture may be obtained by using mixtures, particularly C3/C4 mixtures. Thus, enhanced within-field crop diversity can make an important contribution to sustainable increases in food production.