Indonesian passport holders: 3 person: Jkt-Senzhen by Airasia, SZX-SF by air China

Yes, you are definitely eligible for 24 hour visa free transit. There is no problem regarding the fact that you have separate tickets because you will be issued a temporary entry permit upon your arrival, i.e. you will apply for one at 24 hour visa free transit counter. It is free of charge.

By the way, I have noticed that people are quite confused because of some Timatic quotations. There it is written:

"This TWOV facility does not apply at Fuzhou (FOC), Huangshan (TXN), Mudanjiang (MDG), Shenzhen (SZX), Urumqi (URC) and Yanji (YNJ)."

Anyway, if you are confronted with this detail, you will just tell to the airport personnel to continue reading where they will find the explanation:

This TWOV facility does not apply at Shenzhen (SZX) when passengers are traveling to Hong Kong (SAR China) or Macao (SAR China).

This TWOV facility does not apply at Fuzhou (FOC), Huangshan (TXN), Mudanjiang (MDG), Urumqi (URC) and Yanji (YNJ).

In other words, Shenzhen airport is eligible for 24 hour visa free transit, but not in case when somebody wants to use it for travel to Hong Kong and Macau. It is written quite clumsy, but clear enough for any averagely bright official to understand the meaning of what is written in Timatic.

So, you are definitely eligible for 24 hour visa free transit in Shenzhen.

Wait, wait... You have mentioned that you will fly from Shenzhen to San Francisco... This is fine, but the problem is that there is no direct flight between Shenzhen and San Francisco and since you are flying by Air China, I assume that you will have an additional landing within mainland China. You should present us also about this detail because this is the detail that could affect your eligibility for 24 hour visa free transit! Be very careful and just share with us your real travel plan in its entirety because like this we have done just a first half of determining whether you will be eligible or not for this visa free transit option. So, we are waiting the rest of your itinerary with specific times. Thanks.

My detail flights:
Jakarta - Shenzhen by Air Asia, ETA 14 Dec 22:50
Shenzhen - Beijing by Air China, ETA 15 Dec 10:45
Beijing - San Fransisco by Air China, ETD 15 Dec 16:00
Return Flight:
SF - Beijing by Air China, ETA 05 Jan 18:10
Beijing to Shenzhen by Air China, ETA 05 Jan 23:50
Shenzhen to Jakarta by Air Asia, ETD 06 Jan 11:25
Am I eligible for TWOV 24 hours free? how to apply in Shenzhen or Beijing airport? Usually take how many hours to apply on site?
Please Advices. thank you.

This is all definitely eligible for 24 hour visa free transit both ways :)

You will also print out your flight tickets and have those printouts with you!

For your first travel leg, you will apply for a temporary entry permit in Shenzhen and that could take roughly not more than one hour.

On your way back, you will apply in Beijing and there the waiting time could be also about one hour, but you should also count on waiting time in Beijing for up to two hours.

You will be definitely fine and I suggest you to be at Jakarta and San Francisco airports at least 3 to 4 hours before your scheduled departure because the airport staff sometimes takes quite a time to inspect your tickets, especially when they are not so familiar with visa free transit policy of China.