HRT team principal Colin Kolles will part company with the Spanish team on Thursday after two years at the helm.
A statement said the move was "due to the new direction the team has taken and the decision of the new management to move the headquarters to Spain."
HRT, who have not scored a point since making their debut in 2010, were taken over by Spain's Thesan Capital in July.
Veteran Pedro de la Rosa will return to racing with the team in 2012, but his team-mate has yet to be confirmed.
The statement added: "HRT F1 Team would like to thank Dr. Colin Kolles for his work and dedication throughout these past two years and wish him the best in his future projects."
Kolles, 44, stepped in to replace team founder Adrian Campos ahead of their debut season in 2010.
At the time, the squad were struggling to get their cars ready for the season opener in Bahrain and arrived in the Gulf State having completed no pre-season testing.
The F1 backmarkers have struggled to come close to scoring a point in their first two seasons and have finished 11th in the constructors' championship in 2010 and 2011, one place higher than Virgin, courtesy of better race finishes.
As they look to improve their fortunes, the Spanish outfit are moving their factory from Germany to Spain and have also appointed former Minardi grand prix driver Luis Perez-Sala as a sports advisor.