Alain, 50, previously won a gold medal as head coach of the under-18 women's team at the IIHF Women's World Championship in January.
He started as a video coach with the women's program in 2007 and later served as an assistant coach for the under-22 and under-18 squads.
"It's always an honour to coach Team Canada, and I can't wait to see what these skilled young athletes can accomplish on the ice in Germany, at what is sure to be a very competitive Meco Cup," said Alain in a statement.
Alain will be joined by assistant coaches Tim Bothwell and Cassandra Turner.
Bothwell, 57, comes to the team after serving as an assistant coach on the senior national team and more recently a skills coach at development and team selection camps.
Turner, 31, won a silver with the under-18 team as an assistant coach at last year's IIHF Women's Championship. She also took gold as a player on the under-22 team at the 2003 Air Canada Cup.