A plant culture box assembly (10) having a box (20) and an upper cover (30). The box (20) includes a bottom portion (21), a first peripheral wall (22), and a fastening portion (23). The first peripheral wall (22) is connected with a peripheral edge of the bottom portion (21), so that an opening (29) is formed between the first peripheral wall (22) and the bottom portion (21). The fastening portion (23) is annularly formed at an external side of the first peripheral wall (22). The upper cover (30) includes a top portion (31) and a second peripheral wall (32). The top portion (31) is mounted to the opening (29). The second peripheral wall (32) is connected with a peripheral edge of the top portion (31) and tightly combined with the fastening portion (23) to enable the first peripheral wall (22), the fastening portion (23), and the second peripheral wall (32) to jointly define an isolated space (40). In this way, the box (20) and the upper cover (30) can have preferable airtight effect therebetween.