The rapid development of cities in the recent 10 years caused a reduction in the cultivated land area, which only accounts for 14% of the total land area in China. Land development and reclamation have been regarded as an effective way to compensate farmland occupation. However, most of the newly reclaimed land has poor soil fertility and suitability; in some cases, the production capacity is only 10–30% of the occupied farmland. In order to ameliorate the soil quality of the newly reclaimed land, this study evaluated the effects of commercial organic fertilizer (0.75, 1.50, and 2.25 kg/m2), mushroom residue (1.50, 2.25, and 3.00 kg/m2), biogas slurry (150, 225, and 300 kg/m2), vegetable cake (0.30 and 0.60 kg/m2), and chemical compound fertilizer (37.50 g/m2) on the pH, moisture content and organic matter content (OMC), available phosphate, total nitrogen, alkaline hydrolysis nitrogen, microbial biomass carbon and nitrogen, and number of total bacteria and phosphate-solubilizing bacteria, as well as the growth of maize seedlings. The results from this study indicate that the soil quality (OMC is an indicator) was ameliorated by chemical and organic fertilizers, in particular commercial organic fertilizers, which caused a 9.35–16.35% increase in moisture content, a 11.56–18.72% increase in pH, a 1.73–2.15 fold increase in OMC, a 338.44–491.41% increase in available P, a 36.80–48.14% increase in total N, a 95.32–128.34% increase in alkaline hydrolysis N, a 92.57–178.38% increase in total bacterial numbers, and a 7.57–20.87 fold increase in microbial biomass carbon compared with the control. The pot experiment further indicated that soil amended with commercial organic fertilizers caused a 20.35–30.55% increase in the height and a 12.50–16.67% increase in the total dry weight of maize seedlings. In addition, representative strains with the ability to dissolve phosphorus and fix nitrogen were successfully isolated using the culture method, and were then identified based on colony morphological observation and 16S rDNA sequence analysis, which help us to not only understand why organic fertilizer has great effect on soil improvement, but also provides beneficial microbial resources for further study.