我用下面这段代码写入xml文件  
 TransformerFactory tFactory =TransformerFactory.newInstance();
  Transformer transformer = tFactory.newTransformer();
  DOMSource source = new DOMSource(doc);
  StreamResult result = new StreamResult(new java.io.File("menu.xml"));
  transformer.transform(source, result);

transformer.setOutputProperty("encoding","GB2312");
or
transformer.setOutputProperty("encoding","GBK");

//输出XML流
  private void outputXML() throws DTreeException {
    DOMSource domSource = new DOMSource (doc);
    StreamResult streamResult = new StreamResult(this.out);

    try {
TransformerFactory transformerFactory=TransformerFactory.newInstance();
Transformer transformer=transformerFactory.newTransformer();

Properties properties = transformer.getOutputProperties();
properties.setProperty(OutputKeys.ENCODING,"gb2312");
properties.setProperty(OutputKeys.VERSION,"1.0");
transformer.setOutputProperties(properties);

transformer.transform(domSource,streamResult);
    }
    catch (TransformerConfigurationException tce) {
tce.printStackTrace();
        throw new DTreeException("TransformerConfigure Exception: "+tce.getMessage());
    }
    catch (TransformerException te) {
te.printStackTrace ();
        throw new DTreeException("Transformer Exception: "+te.getMessage());
    }
  }