"I think it is important to constantly reinforce the unity of Christians at a time when we are confronted by a growing secularism," said Merkel, who is herself the daughter of a Protestant pastor who died earlier this month.
"What the Christian faith has in common should always be remembered," she said in her weekly video podcast.
Merkel also said that she was "particularly pleased" at the prospect of Benedict coming to Germany for his first official visit since being elected pope in April 2005.
During his visit, which begins on Thursday and wraps up Sunday of next week, Benedict XVI will visit Berlin, Erfurt in the ex-German Democratic Republic, and Freiburg.
The 84-year old pope will give 18 sermons and speeches during his 21st trip abroad, according to his spokesman.
The visit is already mired in controversy, with a number of theologians leading vocal criticism over the Vatican's antiquated attitudes.
But Merkel said that the visit was an opportunity to recall how Europe was marked by the Christian faith.
"This is a source of strength which we should encourage through dialogue among the religions," added Merkel, who heads the ruling Christian Democratic Union (CDU) party.