Reference list order in a thesis
There are two systems: list the references in alphabetical order, or list the references in the order they are cited in the text. In my experience, which of these two systems is used depends on the academic field you're in. 

Before computers made searchable pdf files common, the first system was really useful when looking for a specific author or reference in the bibliography, and the second was really useful when looking for where a reference was cited in the text. 

With current technology, I don't think it really matters which system you use, although you should pick one and stick to it. My advice would be to check some other theses submitted to the same department to see how they did it.