【Objective】Acidic soil is not conducive to the formation of water-stable macroaggregates, which in turn affects the level of soil fertility and the normal growth of crops. Research suggests that the application of organic fertilizer is an important way to improve acidic soils, however, the effect of organic fertilizers on the formation processes of acidic soil aggregates remains not clear. Also, there is a lack of evaluation and comparison between different types of organic fertilizers. 【Method】The rare earth oxide tracer method was used to test different organic fertilizers with equal carbon content on purple and red soil for 56 days. Four treatments were set up (no organic fertilizer control as CK; ordinary organic fertilizer as OF; biochar organic fertilizer as BC; and bio-organic fertilize as BO) and used to determine the stability of soil aggregates, the content of organic carbon in each fraction of aggregates, soil respiration, and the turnover path and rate of aggregates.【Results】The results showed that compared with the CK, the addition of organic fertilizer effectively reduced the amount of aggregate fragmentation, promoted the turnover and formation of large aggregates (>0.25 mm), and increased the average weight diameter (MWD) of soil aggregates. The BO treatment had the best effect on improving the stability of soil aggregates, which could be increased by 53.5%～103.35%. Adding organic fertilizer promoted the formation of the 0.25 mm aggregates and by calculating the turnover rate of soil aggregates, it was found that the addition of organic fertilizer reduced the turnover rate of large aggregates and increased the turnover rate of small aggregates (<0.25 mm). It is worth noting that in purple soil, the turnover rate of small aggregates was higher than that of large aggregates, while in red soil, the opposite trend was observed. Also, the addition of organic fertilizer promoted soil respiration and significantly increased the content of organic carbon in individual fractions (P<0.05). The total organic carbon content of different treatments was BC > BO > OF > CK, which increased by 14.50%～27.78% in purple soil and only increased by 6.40%～9.82% in red soil. 【Conclusion】In general, the application of organic fertilizer can effectively reduce the fragmentation process of aggregates, promote the turnover of small aggregates to large aggregates, and improve the stability of aggregates. The application of bio-organic fertilizer was more conducive to improving the level of soil water-stable macroaggregate structure, increasing soil stability, and improving soil structure.