Excessive phosphorus accumulation drives eutrophication in aquatic ecosystems, and modified hydrogels have emerged as promising materials for phosphorus removal. However, reported removal performance and optimal operating conditions vary considerably, hindering their transition from laboratory studies to full-scale application. Here, a systematic meta-analysis was conducted to quantify the overall effectiveness of modified hydrogels and identify the major factors governing their performance. Treatment effects were quantified using the natural logarithm of the response ratio (lnRR), with more negative values indicating greater phosphorus reduction relative to the reference condition. Overall, modified hydrogels significantly reduced the phosphorus levels (pooled lnRR = −1.64, 95% CI: −1.73 to −1.55), with inorganic–inorganic modification showing the strongest effect (lnRR = −2.02, 95% CI: −2.16 to −1.88). Coexisting ions, pH, and initial phosphorus concentration were identified as the principal factors contributing to variation in removal performance. These findings provide a quantitative basis for material design and operating-condition optimization and facilitate the practical application of modified hydrogels for phosphorus pollution control. In future, standardized data reporting and long-term pilot- and field-scale validation are still needed to support widespread practical application.