According to the charity, suicide attacks, abductions and beheadings are all "widespread and systematic" and are a means for the Taliban to "instil fear and exert control over the local population".
Teachers, women's rights activists and clerics are among those targeted, with the situation in the south and the south-east particularly grave.
"Afghan civilians are bearing the brunt of this conflict," Claudio Cordone, senior director for research at Amnesty, said as part of the publishing of a report into the situation.
"They are caught in the fighting between the Taliban, Afghan government forces, US forces and forces from other Nato countries.
"But it is the Taliban who have a deliberate policy of targeting civilians - they are killing teachers, abducting aid workers and burning school buildings."
Amnesty cites a recent example of an Afghan journalist, 25-year-old Ajmal Naqshbandi, who was taken hostage last month alongside an Italian reporter, Daniele Mastrogiacomo, and their Afghan driver, Sayed Agha.
Mr Mastrogiacomo was released as part of a prisoner exchange but Mr Agha was beheaded and Mr Naqshbandi had his throat cut last week, according to the charity.
"By using indiscriminate attacks such as suicide bombings in public places and by deliberately targeting civilian workers, the Taliban are committing war crimes," said Cordone.
"The fact that such attacks are widespread and carried out as part of Taliban policy makes them also crimes against humanity."
The Taliban were overthrown after the US-led invasion of the country in October but have continued to retain regional influence, particularly in the south of the country.
According to al-Jazeera, Taliban spokesman Zabullah Mujahid called the report western propaganda.
"The Taliban only target foreign and Afghan military personnel and those who help them," the representative is quoted as saying.
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