Aiming to reveal the fate and transformation mechanism of soil nitrogen under coastal facilities cultivation, three treatments, including subsurface drainage combined with microbial organic fertilizer application (S-OF), subsurface drainage combined with inorganic fertilizer application (S-IF) and inorganic fertilizer application without subsurface drainage (CK) were designed. The model system was grape and rape intercropping cultivation. The distribution of soil total nitrogen in vertical profile, the changes of mineral and organic nitrogen in tillage layer and their correlation with soil physical and chemical properties were observed. The results showed that soil bulk density was decreased and soil porosity was increased under the combination of subsurface drainage and microbial organic fertilizer application;subsurface drainage promoted the transfer of total nitrogen from topsoil to deep soil, and the reduction rate of total nitrogen in topsoil of S-OF treatment was smaller than that of S-IF treatment;more than 80% of total nitrogen in topsoil existed in the organic form, and the proportion of mineral nitrogen was very small, S-OF was beneficial to the increase of mineral nitrogen content in the later stage of the experiment;the mineral nitrogen content in plough layer soil was positively correlated with soil organic matter and total organic carbon. Subsurface drainage and application of microbial organic fertilizer were conductive to improving the soil structure in coastal land, increasing the content of organic matter and total organic carbon in tillage soil, and promoting the transformation of soil organic nitrogen to mineral form. The conclusions can provide scientific basis for the improvement of coastal greenhouse soil and the decision-making of irrigation and fertilization.