While the train from Hung Hom Train Station to Guangzhou is the fastest option, generally, it is not the fastest option for you arrive at the HKIA and wants to go to Guangzhou directly.
From HKIA to Guangzhou ,take a bus instead of a trains. Note that these buses have multiple drops off points in Guangzhou (e.g. universities, China hotels)It is about 2.5-3 hours from HKIA to Guangzhou.
1) By bus: Bus tickets to Guangzhou can be purchased when you arrive at HKIA. It cost about HKD $250 from the Hong Kong airport to Guangzhou. Once you exit HKIA customs, bus counter is right in front of you. Buy ticket, wait 5-10 minutes,and an agent will lead passengers to bus to board. The bus will take you to the border check at Shenzhen Bay. From there you get off the bus with your luggage. And get back on another bus on the other side. You’ll wear a sticker; agents will direct you to the right bus. The next stop is downtown Guangzhou. Typically, the bus will go to 3 different drop off points depending on the schedule. (More information about How to take a bus from Hong Kong airport to Guangzhou )
2) Taking trains: it requires a few transfers because the Airport Express train doesn’t go to Hung Hom Station where the Through Train from Hung Hom (Kowloon) departs for Guangzhou. You need to take the AE train to Tsing Yi, then transfer to Tung Chung Line to go to Nam Cheong, then transfer to West Rail Line to go to Hung Hom. (Hong Kong Metro Map : http://www.mtr.com.hk/en/customer/jp/index.php) Also the A21 Citybus takes you directly from the Airport Ground Transportation Centre to the railway station in Hunghom , which is the last stop of the route, and take about 1 hour. The ticket price is 33hk$. (http://www.hongkongairport.com/eng/transport/to-from-airport/bus_from_hkia.html)
From Hung Hom Train Station you need to go up to the ticket counter to buy tickets for the Through Train (if they are still available). You may not get seats for the next departure as they are in high demand. In any event you would need to wait for the next schedule Through Train . They run about one every hour or so. You go through immigration check at both ends, but do no stop at the actual Hong Kong / China border. The ride takes less than of 2 hours. In total, it would take you probably 4 hours from Hong Kong International Airport to Guangzhou.
The last train departs from Hung Hom at 20:01 . If you miss the last train, take a metro to Luowu from Hung Hom Station(Lo Wu Control Point is an immigration control point of Hong Kong located in Lo Wu, North District, within the Closed Area along the border with mainland China. Its counterpart across the border is the Luowu Port, located within the Luohu District of Shenzhen in mainland China).It is about 45 minutes. After clearing customs and immigration , you can take a train from Luo Wu to Guangzhou there are many trains from Luowu to Guangzhou . (Economic route: Take No A43 Bus from HIKA to Sheung Shui; price is 30.9 HK$ and takes about 75 minutes(last bus at 9:30 pm). Take metro from Sheung Shui to Luo Wu,1 stop , price is 23.5 HK $,and takes about 7 minutes. Take a train from Lowu to Gaungzhou East Railway Station; price is 75 Yuan , and takes about 75 minutes, but there may be a delay waiting at the Lu Wu Control Point )