The blaze started at around 3.30am in the unit at Hong Shing Court in Sun Hing Garden.
Firefighters arrived at the scene and found a 31-year-old man had died after falling from the block.
Inside the flat, rescuers found an unconscious 62-year-old woman who was confirmed dead after she was rushed to hospital.
Police said they had received reports that there was an explosion at the unit, and officers said they found it unusual and will look into it.
Some 350 residents were evacuated.