Posts relating to WikiLeaks were the most common form of attack on social media for the Democratic candidate, who was also heavily criticised on Twitter over an FBI investigation into her use of a private email server, researchers said.
Researchers from the University of Edinburgh in the UK used computer analysis to study the top viral tweets each day between September 1 and November 8 last year
They found that there were three times as many posts attacking Clinton than posts in her favour.
By contrast, viral tweets relating to Trump were split equally in favour and against his campaign.
Posts from Trump's social media campaign and his supporters had a more positive tone than that of his rival, with effective reach for slogans, policy promises and campaigning for swing states.
Trump was criticised for his performance in election debates more than his links to scandals such as the Access Hollywood tape.
Trump supporters were more likely to share news reports from less credible sources, the study found.
In all researchers analysed almost 3,500 posts, which together were retweeted more than 25 million times. Tweets were labelled as being favourable to Trump, Clinton, or neither.
They used data from TweetElect.Com, which collates the most retweeted posts related to the US election.