Maize-peanut intercropping is an important element of China’s agricultural planting model, as it confers ecological benefits, promotes species diversity, and increases economic efficiency and yield. The aim of this study was to explore the yield differences between intercropping and monoculture, and to determine the mechanism underlying the high yield efficiency of the intercropping system using the 13C isotope tracer labelling method. The early maturing corn hybrid Denghai 618 and the early maturing and high-yielding peanut variety Huayu 22 were used as test materials. Three kinds of planting methods were employed, i.e. the sole maize (SM), the sole peanut (SP) and maize–peanut intercropping (intercropped maize, IM; intercropped peanut, IP), for two consecutive years. IM increased yield by 59.7% and 62.3% comparing with SM in 2015 and 2016, respectively. IP reduced yield by 31.3% and 32.3% comparing with SP in 2015 and 2016, respectively. IM significantly increased the photosynthetic rate, leaf area, 13C assimilation distribution, and dry matter accumulation of summer maize, which led to an increase in kernel number, resulting in an increased yield. The decrease in intercropped peanut yield was mainly caused by a decrease in the percent of plump pod and number of pods per plant. The decrease in peanut yield did not affect the production of intercropping, because of the large intercropping advantage and land equivalence ratio. Maize-peanut intercropping provided greater economic benefits than monoculture. These results showed the utility of the peanut-maize intercropping model.