Can we list papers/Journals in reference section, but do not quote them in thesis. It may happen that I read some papers which are close to my area of work, but I may not use any idea from that paper. So in such case, I may not quote anything from that paper. But since I have read that paper, can I list that paper in reference section?
Many journals require you to reference every entry in your list of references somewhere in the paper. That is probably also a good rule of thumb for a thesis.
The reason for this rule is that people do not typically just read through the list of references by itself. They read through the text, and in places where another publication is referenced, they will look it up in the list of references at the end. If the list of references contains entries that are not in fact referenced anywhere in the text, nobody is likely to ever look at that entry.
In practice, if you think that a paper is relevant for your thesis, then there ought to be a place in your text where you should cite it. If you cannot find a place where it would be worthwhile to cite it, then the paper is likely not relevant.
The correct answer for you will depend on your field's citation style. In styles more common in the humanities, you might have a Works Cited section, a Works Consulted or just Bibliography section (MLA style), which together work quite different than APA/IEEE/ACM styles.
The Works Cited section works as the Reference section does in APA/IEEE/ACM style, and only the works cited section needs in-body citations. If you do not cite and properly integrate the work into the body of your paper, you do not include it in the works cited/reference section.
However, some styles and fields use the concept of a more general "Works Consulted" or "Bibliography" section, and listing here does not require you to cite it in the body of the text at all. Here you are explicitly required to include any materials you read, consulted, or which may have materially contributed to your work, even though they were not explicitly cited, quoted, or more directly referenced. This style of work believes in acknowledging much more generalized/abstract "indebtedness", and proponents of this practice often argue that it is more scholarly honest. In fields that don't use it, the argument tends to be that it's overkill, unproductive, and unnecessary, and thus is not used. The fields that use this style also tend to allow secondary sources, and thus both primary and secondary sources end up being listed somewhere even if you only cite the primary source.
You should refer to your own field's style guide and norms, or other explicit rules of your program and institution, to determine what is required of you in your work. In fields where you must actually reference the work directly in the text, it is not appropriate to "stuff the references" with work you did not cite directly. In fields with works consulted/bibliography sections, it can be considered plagiarism and scholarly dishonesty to not list items that you did not even explicitly reference in the text body.