At the party conference in Liverpool, he said Christians on the Left had done good work in their campaign to stop tax avoidance.
"I'll congratulate the Christians on the Left for their campaign promoting the hashtag 'patriots pay their taxes'," said McDonnell.
"It's a great slogan. Patriots should pay their taxes. Labour are already setting the pace on tackling tax avoidance and tax evasion."
Christians on the Left said its campaign was to promote the positives around paying taxes.
"As upright and godly citizens, in respecting our democratically-elected leaders, we should pay our fair share of tax. So should everyone else," the website says.
Chairman Andy Flannagan told Premier's News Hour he was delighted their efforts had been noticed: "We've been working really hard around conference to get people signed up to the campaign, scribbling on little white boards the reason why they're actually really proud to pay tax.
"It's trying to reframe the discussion around tax and make people proud and happy to be doing so. Making the point that it's a patriotic thing to do, to pay tax."
Mr McDonnell confirmed his ambition to shake up the tax system to shift the burden "away from those who earn wages and salaries and on to those who hold wealth".
Setting out his plans for more state intervention in industry, he said: "We need a new deal across our whole economy, because whatever we do in Britain, the old rules of the global economy are being rewritten for us."
The shadow chancellor also promised to enshrine in law a "real living wage" expected to be more than £10 an hour.
Labour would create a living wage review body with a remit to ensure that the minimum income is set at the level needed for a decent life, which he said was likely to be higher in 2020 than the £10 level he proposed last year, he announced.
There would also be a £250 billion national investment bank to support British industry and create a "manufacturing renaissance" following withdrawal from the European Union.