Take about three to five Red Pikmin and go into the corner directly next to Empress Bulblax. Start to throw all the Red Pikmin on it. When it is about to shake them off, whistle your Pikmin back and go into the corner, pressing the C-stick
Down, so they will be behind you and therefore will not be crushed. Keep repeating those steps until you defeat Empress Bulblax. This is a good strategy to use to keep most of your Pikmin alive.