The effects of different associated crops on the structure of endophytic microbial community in tomato roots were analyzed to study the diversity and structure of endophytic microbial community in tomato roots， and to explore and develop the functions of beneficial microorganisms. Five associated crops and monoculture treatments including tomato associated lettuce（A）， amaranth（B）， cabbage（C）， chive（D）， mint（E） and monoculture（F） were set under the same conditions. The structures of endophytic microbial community in tomato roots were analyzed with MiSeq high-throughput sequencing technology. The results showed that Streptomyces， Burkholderia-Caballeronia-Paraburkholderia， Devosia， Nocardioides and Massilia were the top five common dominant endophytic bacterial genera in roots of tomatoes under associated and monoculture systems. However， Noviherbaspirillum was the special dominant endophytic bacterial genus in roots of tomatoes under tomato companioned lettuce （A） associated system； Meanwhile， Actinoplanes was also the unique dominant endophytic bacterial genera in roots of tomatoes under tomato companioned amaranth （B） associated system. Moreover， Herpetosiphon was the special dominant endophytic bacterial genera in roots of tomatoes under tomato companioned chive （D） associated system.Furthermore， Microbacterium was the special dominant endophytic bacterial genus in roots of tomatoes under tomato companioned mint （E）. By contrast， Bacillus， Marmoricola and Glycomyces were the unique dominant endophytic bacterial genera in roots of tomatoes in monoculture system（F）. In addition， Olpidium， unclassified_o_Sordariales and unclassified_p_Ascomycota were the common dominant endophytic fungal genera in roots of tomatoes under associated and monoculture systems. And lmmersiella was the special dominant endophytic fungal genera in roots of tomatoes under tomato companioned lettuce （A） associated system； Meanwhile， Candida， unclassified_c_Agaricomycetes， Phialemonium were the unique dominant endophytic fungal genera in roots of tomatoes under tomato companioned amaranth （B）； Geminibasidium， Plectosphaerella and Rhizophagus were the unique dominant endophytic fungal genera in roots of tomatoes under tomato companioned cabbage （C）； unclassified_p_Chytridiomycota， unclassified_f_Ceratobasidiaceae， Ceratorhiza， unclassified_o_Boletales， and unclassified_p_Basidiomycota were the special dominant endophytic fungal genera in roots of tomatoes under tomato companioned chive （D）； By contrast， Gibberella was the unique dominant endophytic fungal genera in roots of tomatoes under monoculture system （F）. It is indicated that the compositions of dominant endophytic bacteria and fungi at phylum or genera level in tomato roots can be altered by associated cultivation with other crops in comparison with the monoculture of tomato. The special dominant endophytic bacterial and fungal genera can be enriched by associated with other crops. The composition of specific dominant endophytic microorganisms enriched by associated cultivation has the potential to enhance the resistance of tomato to environmental biological or abiotic stresses.