Preheat the oven to 400 degrees F (200 degrees C). Line a 9-inch deep-dish pie pan with one pie crust. Set second pie crust aside.

Bring a large pot of salted water to a boil. Add potatoes and cook until tender but still firm, about 15 minutes. Drain, cool, and chop.

In a medium saucepan, cook onions, garlic, and butter over medium heat until onions become transparent.

Add onion mixture, salmon, and thyme to cooked potatoes. Mash all together with milk, adding just enough to bring about a mashed potato consistency. Season with salt and pepper. Spread evenly into the bottom pie crust.

Place second pie crust over top of salmon mixture. Cut slits into top crust, then pinch edges of both crusts together. Bake on lower rack of oven for 45 minutes.