In the irrigation desert soil of Gansu Hexi inland irrigation area, the field experiment method was conducted to study the effects of functional fertilizer on soil physical properties, microorganism amount and optimal fertilization of seed-production corn field. The results showed that the influence factors of maize yield was in the order of CO (NH2) 2 > (NH4)2HPO4 > resistance to continuous cropping agent and polyvinyl alcohol. The optimal combination was A3B2C1D1 (resistance to continuous cropping agent 30 kg/hm2, CO (NH2)2 600 kg/hm2, and (NH4)2HPO4 350 kg/hm2, polyvinyl alcohol 30 kg/hm2). The application amount of functional fertilizer had linear positive correlation with total porosity, capillary porosity, noncapillary porosity, aggregate and microbial quantity while had linear negative correlation with soil bulk density. With the increase of functional fertilizer application gradient, corn marginal output and profit margins decreased. Earnings appeared negative value when the application amount of functional fertilizer increased by 337.50 kg/hm2 on the basis of 1350 kg/hm2. The regression equation of fertilizer response between application amount of functional fertilizer and corn yield was: y = 3782.61 + 1.6505 x - 0.000 378 7 x2, the optimal application amount of functional fertilizer (x0) was 1 350.01 kg/hm2 with corn theoretical yield (y) of 6 700.99 kg/hm2. The calculation results coincided with best surveyed test treatment 5.