我试了好长的时间都执行不正确，于是采用折衷的方式解决了，那就是写成脚本文件，在执行脚本就没有问题了。如果需要传入参数，从程序中传入就可以了。如下所示：

String script = application.getRealPath("/script/windows/cpu.bat");
String output = application.getRealPath("/temp/windows/cpu.txt");

System.out.println(script);
System.out.println(output);
try {
Runtime.getRuntime().exec(
new String[] { script, output });
} catch (Exception ex) {
ex.printStackTrace();
}

File file = new File(output);
BufferedReader reader = null;
try {
reader = new BufferedReader(new FileReader(file));
String tempString = null;
int line = 1;
while ((tempString = reader.readLine()) != null) {
out.println(tempString + "
");
line++;
}
reader.close();
} catch (IOException e) {
e.printStackTrace();
} finally {
if (reader != null) {
try {
reader.close();
} catch (IOException e1) {
}
}
}