@Configuration
public class SetProperties {

    /**
     * application.properties加载完毕后执行
     * @throws IOException
     */
    @PostConstruct
    public void init() throws IOException {
        //文件夹中读取
        InputStream inputStream = new FileInputStream("D:/*/*/*/config/my.properties");
        BufferedReader br = new BufferedReader(new InputStreamReader(inputStream));
        String line;
        Map<String, Object> map = new HashMap<>();
        while ((line = br.readLine()) != null) {
            //配置项不等于"" 并且排除注释配置项,并将读取到的配置项转成map集合
            if (!line.equals("") && !line.substring(0, 1).equals("#")){
                String[] split = line.split("=",2);
                if (split.length >0){
                    map.put(split[0],split[1]);
                }
            }
        }

        //配置文件名
        String fileName = "application.properties";
        
        //classpath 类路径
        String filePath = PropertiesUtil.class.getClassLoader().getResource(fileName).getFile();
        filePath = URLDecoder.decode(filePath, "utf-8");

        //配置项集合
        Properties props = PropertiesLoaderUtils.loadProperties(new ClassPathResource(fileName));
        
        for (Map.Entry<String,Object> entry : map.entrySet()){
            //修改相同key的值，值为文件夹map的vlaue
            //没有相同的key，会做添加操作
            props.setProperty(entry.getKey(), (String) entry.getValue());
        }
        
        //写入流
        BufferedWriter bw = new BufferedWriter(new OutputStreamWriter(new FileOutputStream(filePath)));
        props.store(bw, "");
        bw.close();
    }

}

注：需要每次重启服务，在考虑不损耗资源的情况下，可以使用定时任务