The appropriate use of manure is important for the sustainable development of dairy farms. To identify more advantageous ways of using manure and key factors in the recycling process, this study investigated differences in soil fertility between solid and liquid manure waste recycling at an integrated farm. Both types of manure waste recycling promote soil fertility. However, solid manure exerted a more pronounced effect on soil fertility, especially on available phosphorus (P), which increased by 93.83%, but only 26.67% with liquid manure. As the amount of solid manure was increased, a clear logarithmic relationship (correlation coefficient = 0.90) formed between manure use and available P, indicating that P was a key index for manure recycling. Solid manure had a more positive influence on soil fertility in terms of microbial community change, as revealed by redundancy analysis and Pearson’s correlation analysis. The results of this study can be applied to most large-scale breeding farms, that the combination of solid and liquid manure fertilizer can be used to meet sustainable development goals. And the findings highlight solid manure as a key component for improving soil fertility.