I had to indent your code before I was able to read it. Then I simplified it a bit, so that I could execute it (I needed a substitute for your data file):

#!/usr/bin/perl

use warnings;


$putword=0;
$q63=7;

&getfile("query63.txt");

sub getfile   {
    @data=(1);
    for($i=0; $i<=$#data;$i++){

    $index=$i;
    @words=split(/\s+/,$data[$index]);
    if(3==2)  {   
        if (1 != 0){
        }
    }
    else {

        @words = split(/\s+/,$data[$index]);
        %query=(2 =>{ctf=>5,
                df=>5,
                1=>{doclen =>42,
                        tf =>5,
                }
                    },
        );
            #When I write here,I can get value..here inside the loop  
+ 
        print "inside ",$query{2}{1}{doclen},"\n";
    }
    }

    #when I write here,I got nothing,,this is outside of loop..
    print "outside ", $query{2}{1}{doclen},"\n";
}

# prints:
#inside 42
#outside 42
[download]

The output was as expected quite sensible. So if you don't get anything outside the loop, your loop probably deleted or overwrote again the data it printed inside the loop

Very good advice from toolic, especially Data::Dumper should help you greatly in finding the problem.