The Britain-based Observatory, which tracks the conflict using sources on the ground, took down its website after the online attack from a group calling itself "The Cyber Army of the Khilafah".
The cyber attackers had posted the face of Observatory director Rami Abdulrahman superimposed over a hostage wearing an orange jumpsuit and kneeling next to an Islamic State militant holding a knife, according to the SITE monitoring service.
Islamic State, which holds large tracts of northern and eastern Syria, has posted several videos showing captives in orange jumpsuits being beheaded, including journalists and aid workers.
"They are trying to stop us," Abdulrahman said by telephone, confirming the SITE report.
"When you work in human rights, you know you get such threats but never like that. It is a serious message."
The hackers also posted a message in English and Arabic using threatening and derogatory language in reference to the rights group, which is one of the most comprehensive observers of the war and a major source of information on the ground.
The Observatory has received letters, tweets and emails from Syrian government and supporters of extremists in the past threatening to kill them but this complex cyber attack was unprecedented, Abdulrahman said.
The cyber attack comes two days after Islamic State released a video which purported to show two young Syrian activists being killed with gunshots to the head in the northern Syrian city of Raqqa, a jihadist stronghold.
The activists, dressed in orange jumpsuits, were accused of spying.
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