Comments for 日, Page 4

Well, of course there are some principals depending on the way the word is made such as if the kanji is combined with hiragana in which case mostly you use Kunyomi or if the word is made from two or more kanji without any hiragana, you use Onyomi. If the kanji is by itself, then most probably Kunyomi would be the reading.

But I generally agree with the point made in the previous post that you must learn it based on experience. Because knowing principals, though necessary, is not exactly going to make you fluent in reading Kanji.

in both onyoumi and kunyoumi there is no reading as NI for this kanji, but NIHON (Japan) why it is spelling NI here? 

I think it is because NIHON (にほん) is an abbreviation of NIPPON (にっぽん).  The 「にっ」 reading in にっぽん is derived from the onyomi reading にち which you would see in words like 日曜日 (にちようび).

Just be aware though that there is a lot of special readings for certain words where there will be no associated kun'yomi or on'yomi for it.  明日 (あした) is an example of this.