did you recognize that there are two variables called temp in your sub?
$temp is used nowere, instead you use only %temp.
i changed your code a bit, so it looks like this

use strict;
use warnings;


my $hash = test::this();
for my $box (keys %{$hash}){
  print "this is box $box\n";
  for my $par (keys %{$$hash{$box}}){
    print "this is partition $par\n";
#    for my $sec (keys %{$hash->{$box}->{$par}}){
#      print "this is section $sec\n";
#    }
  }
}

package test;

sub this
{

my $Dbox = "Dbox";
my $DDD  = "DDD";
my %temp;
$temp{"Dbox"}{$DDD}= "DDD";
for my $box (keys %temp){
  print "this is box $box\n";
  for my $par (keys %{$temp{$box}}){
    print "this is partition $par\n";
#    for my $sec (keys %{$temp{$box}->{$par}}){
#      print "this is section $sec\n";
#    }
  }
}

return \%temp;
}
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use always use strict; use warnings; when you are messing around with things you dont fully understand.
read perlreftut and perldsc->HoH.