To address the issues of soil nutrient deficiency and restricted growth faced by Bougainvillea in urban bridge greening, this study aims to clarify the application effects and optimal fertilization strategy of fish protein fertilizer. Using the common urban bridge greening variety Bougainvillea ‘Miss Manila’ as the test material, five fertilization treatments were established: organic fertilizer (T1), seaweed fish protein fertilizer (T2), polypeptide fish protein fertilizer (T3), organic fertilizer + seaweed fish protein fertilizer (T4), and organic fertilizer + polypeptide fish protein fertilizer (T5), with no fertilization as the control (CK). A pot experiment was conducted to investigate their effects on the growth, root traits, soil nutrients, and enzyme activities of Bougainvillea. The results showed: (1) Fertilization treatments significantly promoted the plant height, ground diameter, crown width, and biomass accumulation of Bougainvillea. Compared with CK, T1 notably increased the north-south crown width (31.30%) and total root nitrogen content (97.79%). T2 exhibited the most pronounced promotion effect on underground biomass, with a remarkable increase of 221.12%. T3 significantly improved ground diameter (24.61%) and leaf SPAD values (13.68%), while T4 showed the most outstanding enhancement in plant height (44.67%) and aboveground fresh weight (80.65%). Additionally, T5 led to a 40.90% rise in total root phosphorus content. (2) All fertilization treatments markedly stimulated root system development. Specifically, T2 increased total root volume, whereas T4 outperformed in multiple root metrics, including total root length, root tip number, total volume, surface area, projected area, and average diameter. (3) Compared with CK, T1 significantly elevated soil organic matter (275.83%), available nitrogen (103.76%), and available potassium (133.09%). T2 boosted total soil potassium content by 53.21%, while T5 sharply increased total phosphorus (142.84%) and available phosphorus (109.82%). Furthermore, T1 enhanced soil neutral protease activity by 144.61%, and T2 improved neutral phosphatase and urease activities by 55.88% and 251.55%, respectively (P<0.05). (4) Principal component analysis and Mantel test results demonstrated that the growth-promoting effects of fish protein fertilizer on bougainvillea were significantly positively correlated with the improvement of soil physicochemical properties and the effective regulation of soil enzyme activities related to carbon, nitrogen, and phosphorus cycling. Compared with polypeptide fish protein fertilizer, the seaweed fish protein composite fertilizer exhibited superior comprehensive effects in enhancing Bougainvillea growth and improving soil fertility. This study provides a scientific basis for high-quality cultivation of plants used in urban three-dimensional greening, and future field trials can be conducted to further verify the fertilizer efficacy.