Objective of investigation: Integrated ecological farming combines rice growth and aquaculture, and is an effective way to improve soil productivity by increasing soil nutrient supply and reducing agricultural non-point source pollution. We investigated the impacts of cultivation patterns, including integrated ecological farming (IEF), rice and vegetable rotation pattern (RVP), and conventional rice cropping pattern (CRP), on the characteristics of soil phosphorus in the Pearl River Delta (PRD). Experimental material: The study area was located in Zengcheng District, Guangzhou City, China. Method of investigation: Tiessen’s classification was used to analyze soil phosphorus fraction contents and its availability. Data collection: Following rice harvesting, topsoil (0–10 cm) and subsoil (10–20 cm) were collected from each field via an S-shaped 5-point sampling method, and the collected samples were mixed into a single sample. Result and conclusions: SOC and phosphorus fractions were significantly influenced by cultivation patterns; IEF significantly increased SOC and phosphorus in the soil. Soil phosphorus was dominated by moderately labile P (40.67–49.41%). IEF also significantly increased soil microbial biomass carbon, phosphorus, and acid phosphatase (ACP) by 67.68, 46.68, and 15.87% compared to RVP, and by 134.14, 65.99, and 30.20% compared to CRP, respectively. SOC and ACP were the primary factors influencing the conversion and effectiveness of soil phosphorus. The integrated ecological cropping pattern can alleviate low phosphorus activity in PRD paddy soils while promoting a sustainable soil nutrient cycle within the ecosystem and guiding the sustainable development of rational soil fertilization in the region.