Pinus massoniana is an important timber tree species in southern China, and acid aluminum stress seriously endangers its growth. This study focuses on physiology, gene regulation and root exudates. Aluminum stress increased the activity of malondialdehyde (MDA), proline (PRO), peroxidase (POD), soluble proteins (SP), soluble sugars (SS) and superoxide dismutase (SOD) in P. massoniana seedlings, and led to changes in growth. We identified hub genes (UCHL3, TCP1, SEC27, GluRS and ACTF) responding to aluminum stress of low concentration and hub genes (RGP, MPT, RPL24, RPL7A and EC3.2.1.58) responding to aluminum stress of high concentration. Aluminum stress mainly affected phenylpropanoid biosynthesis and flavonoid biosynthesis, and it may alleviate aluminum toxicity by inducing the upregulation of genes such as CHS, COMT, DFR and LAR to enhance root exudation of catechin. These results lay the foundation for in-depth studying the molecular mechanism of P. massoniana aluminum stress.