Abstract: The paper aims to enhance stress resistance of seedlings and improve the survival rate of afforestation in difficult sites of island. The effect of microbial fertilizer on seedling growth, biomass and nutrient status of Cinnamomum japonicum var. chenii and Machilus thunbergii were studied by using different kinds and amounts of microbial fertilizer. The results showed that: there was no obvious effect on the growth and biomass accumulation of C. japonicum var. chenii by using different kinds and amounts of microbial fertilizer, but microbial fertilizer could significantly improve the height, diameter and biomass accumulation of M. thunbergii, among them, the growth of height increased by 36.39% and 33.76%, the growth of diameter increased by 17.63% and 15.40%, the total biomass increased by 57.04% and 56.50% by using 40 g and 60 g per pot of bio-gain microbial fertilizer, and the growth of the two species was significantly inhibited by only using high N concentration microbial fertilizer. Microbial fertilizer was beneficial to improve the accumulation of N and P in roots and stems of C. japonicum var. chenii, and substantially enhanced the accumulation of N, P and K of M. thunbergii. The N concentration in roots of C. japonicum var. chenii respectively increased by 13.87% and 17.65%, by using 20 g and 40 g per pot of bio-gain microbial fertilizer, and P concentration in stems respectively increased by 13.39% and 12.60%, while respectively increasing by 27.29% and 11.48% in roots, the trends were consistent between the content change of N, P, K and the concentration of microbial fertilizer; the N concentration in roots of M. thunbergii respectively increased by 10.53% and 27.32% by using 40 g and 60 g per pot of bio-gain microbial fertilizer, and P concentration respectively increased by 47.78% and 70.82%, and K concentration respectively increased by 24.74% and 35.99%. Therefore, the content increased significantly.