I would like to know about the possible differences in describing the content (materials and methods, discussion and conclusion, etc.). How one should justify the thesis and research paper in terms of content?
A research paper may involve only secondary research, whereas a thesis-book will usually report on both primary data (data you collect yourself) as well as secondary data. For example, a research paper may be a review paper.
A research paper might be from 6 to 12 pages long. A thesis-book is roughly from 60 to 600 pages long.
So you see that a thesis-book is really a scaled-up version of a research paper. They will both have an Introduction, Materials and Methods, Results, Discussion, and Conclusion. In the paper, each of these will be a section. In the thesis-book, each will be a chapter. Sometimes a thesis-book can be constructed from several papers, but I don't think that you are there yet.
Since the thesis-book is a publication with limited circulation, you have the opportunity to go into as much detail in it as you feel necessary. For example, you could include all your data in a long appendix. In the paper, however, you are limited to the amount of space you have available to you. So you have to make every inch count.
The time scale for the full production of a research paper might be three months; that for a thesis-book would be 2 to 3 years.
Shall I incorporate each and every technical details of work in thesis? I am asking especially for the section materials and methods. Is it justifiable to only cite the method? Or Shall I give the details of the same?
If the method that you used has a name, you just give the name. If you needed to deviate from standard procedure, then you need to document your deviations. Briefly, you give enough detail for a qualified researcher to replicate your work. By selective referencing, you can eliminate the need to reproduce mundane detail.
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