There were three things about the Spider Queen's final phase that were important to remember.
Firstly, it undid all restrictions placed upon her, which included Jax's poison threads. So if he wanted to use his poison threads to kill it again, he would have to place them on it again.
However, considering it was at the top of the giant tree, that would be quite difficult.
Secondly, it would release all of its remaining spiderlings to fight its enemies while it stayed in the trees. There were between 15 to 20 spiderlings each time it appeared, and depending on how long the previous phases took, one wouldn't have to fight that many.
Jax, however, had forced it to go through its second phase quite quickly, and as a result, he still had 13 spiderlings to go through.
The last thing Jax needed to remember was to dodge any poison attacks that came from the sky. Since the Spider Queen wasn't going to come down, it would instead start dripping venom onto its enemy.