Thylakoids host a large number of proteins to confer photosynthesis and chemical biosynthesis essential for plant survival and growth. Successful isolation of high-quality thylakoids is the first step to studying the compositions and function of thylakoid protein and metabolites. Nevertheless, former studies isolated chloroplasts and thylakoids using a high-speed centrifuge with Percoll, which was expensive and unfriendly to the environment. The method presented here aims to establish a simple and inexpensive method to isolate high-quality thylakoids for protein analysis by utilizing sucrose instead of Percoll to reduce the cost and modify the centrifuge speed into the range usually used in labs.