China has implemented large-scale mangrove restoration and afforestation initiatives in recent years. However, there has been a paucity of research on the growth of mangrove seedlings in a composite stress environment and the allometric growth equation of mangrove seedlings. To enhance juvenile mangrove survival rates and develop precise carbon sequestration models, this study examines biomass accumulation patterns and allometric equation development under diverse environmental and biological conditions. A manipulative field experiment employed a three-factor full factorial design using seedlings from eight mangrove species. The experimental design incorporated three variables: salinity, flooding (environmental stressors), and aboveground interspecific competition (a biological factor). Following a two-year growth period, measurements of surviving seedlings’ basal diameter, plant height, and above- and belowground biomass were collected to assess growth responses and construct allometric models. Results indicated that high salinity reduced total mangrove biomass, whereas prolonged flooding increased tree height. Interspecific competition favored fast-growing species (e.g., Sonneratia caseolaris) while suppressing slow-growing counterparts (e.g., Avicennia marina). Synergistic effects between salinity and flooding influenced biomass and basal diameter, whereas salinity–flooding and salinity–competition interactions demonstrated antagonistic effects on tree height. High salinity, prolonged flooding, and competition elevated the proportion of aboveground biomass allocation. The results suggest that salinity stress and flooding stress were major growth-limiting factors for juvenile mangroves. Slow-growing species are not suitable to be mixed with fast-growing species in mangrove afforestation projects. Allometric models fitting for juvenile mangroves growing under different environmental factors were also developed. This study deepens our understanding of the growth of mangrove seedlings under composite stress conditions, provides effective tools for assessing the carbon sink potential of mangrove seedlings, and provides scientific guidance for future mangrove restoration projects.