Atomic　clock　difference　(errors)　contains　various　kinds　of　noise　and　it　can　be　characterized　to　as　non-stationary.　Hilbert-Huang　Transform　(HHT),　a　new　adaptive　method　based　on　empirical　mode　decomposition　(EMD)　and　Hilbert　spectral　analysis,　was　used　to　analyze　and　process　atomic　clock　difference.　Taking　real　data　for　discussion,　the　results　show　that　HHT　method　is　practical　and　versatile　to　handle　noisy　data　and　characterize　the　clock　behavior.