Aquilaria crassna Pierre ex Lecomte is a principal species renowned for its production of agarwood. However, the active components of agarwood are not universally in compliance with the standards set by the Chinese Pharmacopoeia. We have identified an elite A. crassna tree with agarotetrol and alcohol extract levels that exceed these standards and have successfully established a stable in vitro micropropagation system using stem segments from this elite tree. The effects of auxins and minerals on axillary-bud induction, shoot multiplication, and rooting were investigated. The most effective medium for axillary-bud induction was a half-strength Murashige and Skoog (1/2MS) medium supplemented with 0.50 mg/L 6-benzylaminopurine (6-BA), achieving an induction rate of 53.33% with minimal hyperhydricity. The optimal shoot proliferation medium was an MS medium with 0.40 mg/L 6-BA, yielding a propagation coefficient of 2.96 without hyperhydricity. The best rooting medium comprised quarter-strength MS (1/4MS) macroelements and 1/2MS microelements with 0.10 mg/L naphthaleneacetic acid (NAA), resulting in an 82.54% rooting rate. Substrate effects on transplant survival and growth were also evaluated, and peat soil was identified as the best substrate, achieving a survival rate of 96.67%. This study introduces a straightforward and efficient in vitro micropropagation system utilizing mature A. crassna as explants. It holds significant importance for the consistent production of agarwood that complies with the standards of the Chinese Pharmacopoeia and provides a model for the targeted breeding of medicinal plants.