The Blossoming Flower Clock is an ingenious timepiece made in the 18th century and now preserved in Beijing Palace Museum, China. It generally cannot be disassembled and examined due to its historical value, and hence the inner mechanisms of the clock are unknown. This study provides a systematic design approach for reconstructing the five automata in the clock, namely time keeping, music playing, ducks swimming, flowers blossoming, and figures posturing. For the first two automata, practicable mechanical structures are inferred based on a classification and analysis of known technological customs and practice at the time. A total of seven feasible mechanisms are proposed for the time-keeping automaton, while three possible mechanisms are presented for the music-playing automaton. For the remaining automata, the structural characteristics and design constraints of the associated mechanisms are derived by means of a systematic motion analysis. By applying the concepts of generalization and specialization, a total of seven feasible mechanisms are synthesized for the ducks-swimming automaton, while six mechanisms are presented for the flowers-blossoming automaton and figures-posturing automaton. The proposed methodology is formalized in the form of a flow chart. Overall, the present results suggest that the proposed method provides a useful approach for reconstructing the unknown internal workings of mechanical devices.