Cut squash in half crosswise; remove and discard seeds. Place squash halves, cut side down, in an 11- x 7- x 1 1/2-inch baking dish. Add water to depth of 1/2 inch. Bake, uncovered, at 350° for 40 minutes. Remove from oven, and invert squash halves.
Combine brown sugar and next 4 ingredients in a small bowl, stirring well. Spoon brown sugar mixture evenly into squash halves. Bake, uncovered, an additional 20 minutes, basting occasionally. Sprinkle with pecans.