使用了两种方式，个人更倾向于第二种
方法1：
import java.io.BufferedReader;
import java.io.BufferedWriter;
import java.io.File;
import java.io.FileReader;
import java.io.FileWriter;

public class FileOperation {
    public static void main(String args[]){
        try{
            boolean flag=false;
            BufferedReader br=new BufferedReader(new FileReader((new File("C:/route.txt"))));
            BufferedWriter bw=new BufferedWriter(new FileWriter((new File("C:/result.txt"))));
            String temp=br.readLine();
            while(temp!=null){
                if(flag){
                    bw.write("\r"+"\n"+temp.toUpperCase());
                }else{
                    bw.write(temp);
                    flag=true;
                }
                temp=br.readLine();
            }
            br.close();
            bw.close();
        }catch(Exception e){
            e.printStackTrace();
        }
    }
}

方法2：
import java.io.BufferedInputStream;
import java.io.BufferedOutputStream;
import java.io.BufferedReader;
import java.io.FileInputStream;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.InputStreamReader;
import java.io.PrintStream;

public class FileOperation2 {
    public static void main(String[] args) throws IOException {
        BufferedInputStream in = new BufferedInputStream(new FileInputStream(
                "C:/route.txt"));
        PrintStream out = new PrintStream(new BufferedOutputStream(
                new FileOutputStream("c:/result.txt")));
        System.setIn(in);
        System.setOut(out);
        BufferedReader br = new BufferedReader(new InputStreamReader(System.in));
        String s;
        boolean flag=false;
        while ((s = br.readLine()) != null){
            if(flag){
                System.out.print("\r\n"+s.toUpperCase());
            }else{
                System.out.print(s);
                flag=true;
            }
        }
        out.close();
    }
}