My wife is currently in USA and my wife's son, a 15 years old child with her ex-hu*****and, is currently in China.
Do I need to file I-130 for my wife and her son separately?
-Yes.
According to the I-130 instructions, we need to file I-130 for each relative separately.
-True.
But it seems that this is not reasonable because her son could be automatically eligible for immigration once the I-130 petition for her is approved.
-Not true. You missed understanding of the I-130.
On the other hand, if I file I-130 for her only, it seems there will be also a problem:
She can file I-485, but her son has to go through the Consular process.
-That is not a problem, but it is true.
And in the I-130 form, there are no places to fill in her son's name, telling USCIS that her son needs to go through the consular process.
-You need to file two I-130s, one for your step-son for consular processing (select the CP on the I-130), another for your wife for I-485 filing (select Adjustment of status on the I-130).