With the ref https://stackoverflow.com/questions/20799498/magento-create-partial-invoice-programmatically I have tried but it's occurred only for shipping cost or single sku of multiple sku. I want to create $100 invoice out of $500 subtotal of order. I mean if subtotal is $500 I want to create two separate invoice. one is $100 & another is $400 . Need a help, Thanks in advanced.