//输出output()
public void output() throws IOException {
  FileWriter fw = new FileWriter("D://stu.txt");
  BufferedWriter bw = new BufferedWriter(fw);
  bw.write("name" + "score1" + "score2" + "score3");
  bw.newLine();
  for (int i = 0; i < 5; i++) {
   bw.write("  " + name);
   for (int j = 0; j < 3; j++)
    bw.write("  " + score[j]);
   bw.newLine();
  }
  bw.close();
}

有可能是因为fw没有关闭，在bw.close();后面加句fw.close();试试