A plant culture box assembly is composed of a box and an upper cover. The box includes a bottom portion, a first peripheral wall, and a fastening portion. The first peripheral wall is connected with a peripheral edge of the bottom portion, so that an opening is formed between the first peripheral wall and the bottom portion. The fastening portion is annularly formed at an external side of the first peripheral wall. The upper cover includes a top portion and a second peripheral wall. The top portion is mounted to the opening. The second peripheral wall is connected with a peripheral edge of the top portion and tightly combined with the fastening portion to enable the first peripheral wall, the fastening portion, and the second peripheral wall to jointly define an isolated space. In this way, the box and the upper cover can have preferable airtight effect therebetween.