In southern China, the eucalyptus plantation industry has been severely restricted by government policy over concerns on negative environmental impacts. In its place, large-scale plantations of high-value tropical tree species such as nitrogen-fixing Dalbergia odorifera and hemiparasite Santalum album have been widely cultivated including in mixed-species plantations. However, despite their poor growth, little information is available on suitable silvicultural practices of these plantations. Therefore, we subjected an 8-year-old mixed stand of D. odorifera and S. album to weeding, fertilization, weeding + fertilization, or no (CK) treatments and measured soil microbial biomass, respiration, nutrients, nitrogen mineralization and leaching and tree growth and litter production. Weeding and fertilization decreased microbial biomass but increased soil respiration, inhibited mineralization, had not effect on leaching of soil nitrogen, and improved the nutrient status of plantation soil. All practices improved the growth of D. odorifera. In the mixed plantation, fertilization increased litter production and nutrient content, but weeding and weeding + fertilization decreased growth of S. album and litter production in mixed plantation because weeding decreased the number of S. album haustoria in underground plant roots. In conclusion, fertilization is recommended; however, weeding-related practices are inappropriate for D. odorifera and S. album mixed plantations. These conclusions have important implications for managing other parasite or mixed-species plantations.