They mean pretty much the same thing. I think what would be most helpful is to know which ones are more applicable to certain subjects, and which are used more often.
They all mean "one part of a whole" but:
When talking about food, we use "portion" very often.
Example: I gave each child a portion of the food.
Example: I try to only eat a small portion of dessert.
Section is the most versatile in terms of use. You can talk about a section of a building (like a room or area). Or a section of a website. Or a section of some cloth or other material you're cutting into separate parts. Or a specific part of a book.
Example: Here is the science fiction section of the library.
Example: In this section of the textbook, it talks about verb tenses.
Example: The wood was measured and cut into three sections.
"Segment" is used a lot less often than "section". If you're in a mathematics class and discussing lines, you'll hear "segment" a lot. But otherwise, "section" is usually a better choice.
Example: This segment of the line is on a separate plane.