In a Dutch oven, heat olive oil over medium heat. Add onion, salt, pepper, and thyme, and reduce to medium low. Cook for 30 -35 minutes or until caramelized, stirring occasionally.
Add blueberries, vinegar, brown sugar, honey, and red wine and cook until berries are enlarged and about to burst and liquid is reduced, about 5-10 minutes. Add lemon juice and stir, smashing berries. Remove thyme stems.
Remove from heat and cool to room temperature. Spoon into a clean jar and refrigerate until thickened. Use to top crostini or burgers.