It's (my) favorite time of day. 就括号部分提问

whose favorite time of day is it ?
特殊疑问句中疑问词后用一般疑问句语序,所以is在it前.
whose可以作疑问代词,也可以做疑问形容词.
如:Whose jacket is this? whose作定语.
Whose is this jacket? whose作疑问代词.
你的这句话中whose是形容词性的,作定语.所以is不能放在whose后.给你分析下句子成份:whose favorite time of day 为表语.is是系动词,it是主语.

whose favorite time of day is it ?

很明显是it is

whose在这里是形容词，后面必须有被修饰的名词，即favourite time. is 是系动词，这里充当助动词使用， 在疑问句中它应该放在主语前，即it前。正确答案whose favorite time of day is it ?

一楼说的对