Is a 1997 Malibu engine the same as 2003 engine?

No, a 1997 Chevrolet Malibu engine is not the same as a 2003 Chevrolet Malibu engine. Chevrolet changed engines and platforms across its model years, so even if they both happened to use a V6, for example, the specifics (displacement, internal components, etc.) would be different. There might be some shared components, but they wouldn't be interchangeable without significant modifications (if at all). You'd need to check the specific engine codes for each year to be certain.