So, the Phantom Express is a pretty difficult boss, isn't it? Countless deaths have been inflicted by it, so I'm here to stop it.
So here's the equipment you'll need:
Weapon 1: Roundabout | Weapon 2: Charge Shot | Charm: Smoke Dash (because why not?) | Super Art: Energy Beam
So now, here's how to kill the boss!
This phase is the Pale Man. For Phase 1, you only need to do this: Turn to the left side, jump, and spam Roundabout, stopping only to parry the pink soaps. You will hit virtually all the eyes and kill the first phase before you take damage.
This phase is a skeleton with two hands, which reminds me of Terraria's Skeletron. Don't focus on moving the cart. You don't have to be standing in the right place to dodge. Just use Energy Beam, and it removes most of the phase. Smoke Dash is good here.
This phase is against two...M&Ms? Switch to Charge Shot for this one. First off, move your cart to the left if it isn't already there. Then, spam Charge Shot on the left head. It will die before the second one can finish attacking. Then parry a skull or two, and spam Charge Shot on the right side M&M.
This pits you against the train. The fight requires you to parry the light bulb and then shoot at the moving heart. This can be frantic if you're using a terrible weapon, but you have Charge Shot, and it literally takes four of those to kill the train.
Well that's it, hope this helps you!