© 2015, Springer International Publishing Switzerland. Aims: The function of indigenous mycorrhizal fungi in improving crop growth is not well addressed because of methodological limitations. In this study, we determined the effects of the indigenous arbuscular mycorrhizal (AM) fungal community on the growth responses and salt tolerance of cotton and maize. Methods: Through a 2-year field trial with in-growth microcosms constructed by polyvinylchloride (PVC) tube cores and 30-μm nylon mesh that were buried in different saline soils, two core treatments, static (freely allowed AM fungal colonization) and vibrating (patting the top core edge twice every day to break any extraradical hyphae that intends to access into the core to reduce AM fungal colonization), were applied in field conditions. Results: The results showed that vibration did not affect the growth of the control non-mycorrhizal plant, sugar beet, but significantly affected the growth of the mycorrhizal plants, cotton and maize. These data indicated that such core systems could provide a reliable method to quantify the functions of the AM fungal community in situ. Mycorrhizal colonization of cotton and maize significantly declined in the vibrating treatment compared to the static treatment. Phosphorus (P) uptake and biomass production of cotton and maize were significantly higher in the static than the vibrating. The indigenous AM fungal community promoted leaf proline accumulation in cotton and a higher K+/Na+ ratio via selective preferential uptake of K+ over Na+. These effects and enhanced P uptake derived from AM fungi were related to alleviating salt stress and promoted the growth of cotton and maize in saline soils. Conclusions: Our results demonstrated that indigenous AM fungi play a role in improving crop growth by alleviating the harmful effects of high salinity in intensified cropping systems.