根据guigui111111的建议：先把Map按Key从大到小排序，然后再把Key和Value互换。这也是一种很好的思路，我写了一下代码，顺便贴上来，供大家参考与分享。

package shuai.study.map;

import java.util.Comparator;
import java.util.HashMap;
import java.util.Iterator;
import java.util.Map;
import java.util.Map.Entry;
import java.util.TreeMap;

/**
 * @author shengshu
 * 
 */
public class UniqueMap1 {

	// Transfer to sorted Map
	public static Map<String, String> transferToSortedMap(Map<String, String> map) {
		// Define comparator for TreeMap
		// Note: Sort according to descending, because retain the smaller Key's record when exchanging Map's Key and Value
		Map<String, String> sort_map = new TreeMap<String, String>(new Comparator<String>() {
			@Override
			public int compare(String key1, String key2) {
				return key2.hashCode() - key1.hashCode();
			}
		});

		sort_map.putAll(map);

		return sort_map;
	}

	// Exchange Map's Key and Value
	public static Map<String, String> exchangeMap(Map<String, String> map) {
		Map<String, String> exchange_map = new TreeMap<String, String>();

		for (String key : map.keySet()) {
			String value = map.get(key);

			exchange_map.put(value, key);
		}

		return exchange_map;
	}

	// Print Map
	public static void printMap(Map<String, String> map) {
		Iterator<Entry<String, String>> iterator = map.entrySet().iterator();

		while (iterator.hasNext()) {
			Entry<String, String> entry = iterator.next();

			String key = entry.getKey();
			String value = entry.getValue();

			System.out.println(key + " --> " + value);
		}
	}

	public static void main(String[] args) {
		Map<String, String> map = new HashMap<String, String>();
		map.put("A", "1");
		map.put("C", "3");
		map.put("D", "2");
		map.put("B", "3");
		map.put("E", "3");

		// Sort Map by descending order
		// Note: Sort according to descending, because retain the smaller Key's record when exchanging Map's Key and Value
		Map<String, String> sort_map = UniqueMap1.transferToSortedMap(map);

		// Exchange Key and Value for overlapping repetition record
		Map<String, String> exchange_map = UniqueMap1.exchangeMap(sort_map);

		// Exchange Map for recovering Key and Value, this Map is what we want
		exchange_map = UniqueMap1.exchangeMap(exchange_map);

		// Print Map
		UniqueMap1.printMap(exchange_map);
	}
}