Houston also has retained hitting coach Sean Berry, pitching coach Dewey Robinson, first base coach Jose Cruz and bullpen coach Mark Bailey.
The staff will work under manager Cecil Cooper, who guided the Astros to an 86-75 record last season.
Clark managed Round Rock last year after three years managing the team's Double-A affiliate in Corpus Christi.
Cruz will return for his 13th season as the club's first base coach and 26th overall season within the organization. Cruz played for the Astros from 1975-87.
