Intercropping　systems　can　flexibly　use　resources　such　as　sunlight,　heat,　water,　and　nutrients　in　time　and　space,　improve　crop　yield　and　land　utilization　rates,　effectively　reduce　continuous　cropping　obstacles　and　the　occurrence　of　diseases　and　insect　pests,　and　control　the　growth　of　weeds.　Thus,　intercropping　is　a　safe　and　efficient　ecological　planting　mode.　The　legume-cereal　intercropping　system　is　the　most　common　planting　combination.　Legume　crops　fix　nitrogen　from　the　atmosphere　through　their　symbiotic　nitrogen　fixation　abilities,　and　the　fixed　nitrogen　can　be　transferred　to　and　utilized　by　cereal　crops　in　various　ways.　The　symbiotic　nitrogen　fixation　efficiency　of　legume　crops　was　improved　by　reducing　the　inhibition　of　soil　nitrogen　on　nitrogenase　activity　through　competitive　absorption　of　soil　nitrogen.　However,　the　effects　of　nitrogen　transformation　and　distribution　in　intercropping　systems　and　microbial　community　structure　characteristics　on　nitrogen　transfer　need　to　be　further　explored.　In　this　review,　(i)　we　present　the　transformation　and　distribution　of　nitrogen　in　the　legume-cereal　intercropping　system;　(ii)　we　describe　the　soil　microbial　community　characteristics　in　intercropping　systems;　and　(iii)　we　discuss　the　advantages　of　using　modern　biological　molecular　techniques　to　study　soil　microorganisms.　We　conclude　that　intercropping　can　increase　the　diversity　of　soil　microorganisms,　and　the　interaction　between　different　plants　has　an　important　impact　on　the　diversity　and　composition　of　the　bacterial　and　fungal　communities.　The　extensive　application　of　modern　biological　molecular　techniques　in　soil　microbial　research　and　the　great　contribution　of　intercropping　systems　to　sustainable　agriculture　are　particularly　emphasized　in　this　review.