import java.io.BufferedReader;
import java.io.BufferedWriter;
import java.io.File;
import java.io.FileReader;
import java.io.FileWriter;
import java.io.IOException;
import java.util.Arrays;

public class Test {
    
    BufferedReader br = null;
    BufferedWriter bw = null;
    static String [][] a = null;
    
    public Test() throws IOException{
        br = new BufferedReader(new FileReader(new File("c:"+File.separator+"exp.txt")));
        bw = new BufferedWriter(new FileWriter(new File("f:"+File.separator+"1.txt")));
    }
    
    public void sort(){
        String tmp[];
        for(int i = 1;i < a.length;i++){
            for(int j = 0;j < a.length - i;j++ ){
                if(Integer.parseInt(a[j][0]) > Integer.parseInt(a[j+1][0])){
                    tmp = a[j];
                    a[j] = a[j+1];
                    a[j+1] = tmp;
                }
            }
        }
    }
    
    public void setArray() throws IOException{
        String tmp = "";
        for(int r = 0;r < a.length;r++){
            for(int l = 0;l < a[r].length;l++){
                if(l != a[r].length - 1){
                    tmp = tmp + a[r][l] + ",";
                }else{
                    tmp = tmp + a[r][l] + "\r\n";
                }
            }
            bw.write(tmp);
            tmp = "";
        }
        bw.close();
    }
    
    public String[][] getArray() throws IOException{
        String tmp[][] = new String[1024][1024];
        int num = 0;
        while(br.read() != -1){
            tmp[num] = br.readLine().split(",");
            num++;
        }
        tmp = Arrays.copyOf(tmp, num);
        br.close();
        return tmp;
    }
    
    public static void main(String[] args) throws IOException {
        Test test = new Test();
        a = test.getArray();
        test.sort();
        test.setArray();
    }
}

------解决方案--------------------
用Map试试
key为顺序值
value为一行值

------解决方案--------------------
如果学号等长，而且在行首，对整行排序即可。

Java code
 // jdk7
List<String> conents = Files.readAllLine(path, Charset.defaultCharset());
Collections.sort(contents);
Files.write(path, contents, Charset.defaultCharset());