Addressing the United Nations Human Rights Council, Blinken said Obama will stress the need for democracy and free political expression in Cuba during the March 21-22 visit, the first by a US president since 1928.
"In Cuba, we are increasingly concerned about the government's use of short-term detentions of peaceful activists, which reached record numbers in January," Blinken said.
"We call on the Cuban government to stop this tactic as a means of quelling peaceful protest," he added.
"During his historic visit... President Obama will emphasise that the Cuban people are best served by an environment where people are free to choose their political parties and their leaders, express their ideas, and where civil society is independent," Blinken told the council.
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He began his speech by condemning Russia's rights record, noting the one-year anniversary of the assassination of former deputy prime minister Boris Nemtsov in central Moscow.
"The Russian government's attempts to suffocate civil society, suppress political opposition, and stigmatise members of minority groups, continue unabated," Blinken told the UN body.
The comments came as the two nations were cooperating on efforts to maintain a fragile ceasefire in Syria and push for a breakthrough at peace talks set to resume in Geneva next week.
Asked about his emphasis on Russia, Blinked told reporters that despite joint diplomatic efforts on Syria, it was "critically important" for the US to convey to Moscow its human rights concerns.