There are several methods for preventing chipmunk damage to gardens.

Habitat modification - Where chipmunks are a problem, landscaping features, such as ground cover, trees, and shrubs should not be planted to continuously connect wooded areas with the foundations of homes. Cover provides protection for chipmunks that may attempt to gain access to the home. It also is difficult to detect chipmunk burrows that are adjacent to foundations when wood piles, debris, or ground cover plantings provide aboveground protection. To prevent spilled bird seed from attracting and supporting chipmunks near homes, place bird feeders at least 15 to 30 feet from buildings. Keeping the grass cut short around the edges of buildings will provide less cover for the chipmunks and cause them to use the area less frequently.

Exclusion – Covering the ground with half inch square hardware cloth or chicken wire will prevent chipmunks from burrowing into the ground. A fence two or three feet high of the same material will exclude chipmunks from a garden. Either bury the bottom six inches of the fence material or bend the bottom of the fence six inches out. The bend should be staked down with landscape pins.

Repellents - Taste repellents containing bitrex, thiram, or ammonium soaps of higher fatty acids can be used to protect flower bulbs, seeds, and foliage not intended for human consumption. These repellents are labeled for use against squirrels. Multiple applications of repellents are required. Repellents can be expensive and usually do not provide complete damage reduction to horticultural plantings.

Trapping - Trapping is the most practical method of eliminating chipmunks from many home situations. Live-catch wire mesh traps or common rat snap-traps can be used to catch chipmunks. Live traps can be purchased from local hardware stores or pest control companies or rented from local animal shelters. A variety of baits, including peanut butter, nutmeats, pumpkin or sunflower seeds, raisins, prune slices, or common breakfast cereal grains can be used to lure chipmunks into live traps. Place the trap along the pathways where chipmunks have been seen frequently. Secure the trap so it does not move when the animal enters. Trap movement may set off the trap prematurely and scare the chipmunk away. It is helpful to "pre-bait" the trap for 2 to 3 days by wiring the trap doors open. This will condition the chipmunk to associate the new metal object in its territory with a new free food source. Set the trap after the chipmunk is actively feeding on the bait in and around the trap. Check traps frequently to remove captured chipmunks and release any nontarget animals caught in them. Avoid direct contact with trapped chipmunks. Transport and release live-trapped chipmunks several miles from the point of capture (in areas where they will not bother someone else).

You can find more information from the following article: Chipmunk Control | UGA Cooperative Extension

Thank you for your question and have a great gardening experience.