In the past decades, the application of organ fertilizer in agricultural soils has attracted wide attention. However, few studies have carefully explored the effects of humic acid organic fertilizer on soil microbial colonies, soil enzyme activities, and soil fertility. To provide a better growing environment for crops, we explore the best regulation mode of humic acid organic fertilizer in the farmland in the Songnen Plain Heilongjiang province. Through field experiment, we selected paddy as the test objective and applied humic acid organic fertilizer. Under the condition of water-saving irrigation, five fertilization levels were set up, which were NPK (local nitrogen level, 110 kg.hm-2 pure nitrogen), NPKH1 (450 kg.hm-2 humic acid organic fertilizer + 77 kg.hm-2 nitrogen), NPKH2 (750 kg.hm-2 humic acid organic fertilizer + 55 kg.hm-2 nitrogen), NPKH3 (1050 kg.hm-2 humic acid organic fertilizer + 33 kg.hm-2 nitrogen) and PKH (1500 kg.hm-2 humic acid organic fertilizer). The effects of different humic acid organic fertilizers on soil microbial colonies, soil enzyme activities, and soil fertility were discussed. The results showed that humic acid organic fertilizer could effectively change the structure of soil microbial colonies, soil enzyme activities, and soil fertility. Compared with NPK treatment, the bacteria, fungi, and actinomycete, urease, and catalase in PKH, NPKH3, NPKH2, and NPKH1 treatments increased, and significantly different under 0-10 cm layer conditions (P<0.05). With the increase of humic acid organic fertilizer application, soil organic matter and soil fertility from superior to inferior was PKH>NPKH3>NPKH2>NPKH1>NPK. Therefore, the application of humic acid organic fertilizer was an effective measure to improve soil fertility and increase the amount of soil colony structure and enzyme activities.