Court officials took two days to read out all 626 charges against the 36-year-old divorcee, and finished Thursday afternoon.
They included 599 charges of sodomy against the 15-year-old girl, as well as counts of incest, rape and other sex crimes.
The bespectacled suspect, in a grey T-shirt and blue trousers was calm when the charges were read in court. He pleaded not guilty and the case will now proceed to trial.
"He faces a prison sentence of over 12,000 years," Aimi Syazwani, a deputy public prosecutor, told AFP at a newly-established special court for sex crimes against children in the administrative capital Putrajaya.
For each charge of sodomy, the man can be punished with a maximum jail term of 20 years, as well as caning. He faces a rape charge that carries a maximum sentence of 20 years, and 30 other charges of sexual assault, each punishable by up to 20 years in jail.
The suspect cannot be named to protect the identity of the victim.
The man, who sold investment products, was arrested on July 26 after the girl's mother lodged a police report. The offences were allegedly committed between January and July this year, when the daughter was living with her father.
The special court for sexual crimes against children was launched in June.