A three-member team from New Delhi's All India Institute of Medical Sciences(AIIMS) will perform the second autopsy on Ilavarasan's body.
The team is likely to reach Dharmapuri later on Friday.
According to reports, the court gave the order after two doctors, who re-examined Ilavarasan's body, gave conflicting opinions on his death.
The Tamil Nadu government on Monday formed a one-member judicial commission to probe Ilavarasan's death.
Ilavarasan's body was found along a railway track in Dharmapuri on July 4.
The first post-mortem report of Ilavarasan's body claimed that he died due to a head injury.
His family has alleged that he was murdered.
The police, however, said the man committed suicide.
Amid controversy over Ilavarasan's death, the Madras High Court on July 5 directed the authorities to preserve his body.
The court reportedly said that the video of the autopsy would be shown to Ilavarasan's family. In case, they were not satisfied with it then another autopsy would be performed on the deceased Dalit man's body.
Ilavarasan had married an upper caste Hindu girl Divya Nagaraj last year.
The marriage had triggered anti-Dalit violence in three villages of Dharmapuri in November last after the woman's father committed suicide.
Around 200 huts reportedly owned by Dalits in and around the village where Ilavarasan lived were torched following the death of Divya's father.
Divya later returned to her family and started staying with her mother.
Divya's mother had filed a case in the Madras High Court asking her to be released from "unlawful detention", reports said.
Divya on July 3 told the Madras High Court that she will never go back to her husband.
The court on July 5 directed authorities to give security to Divya and her family.
--IBNS (Posted on 13-07-2013)