G'day bshah,

"Open user.txt and iterate through each user and check each line on ldap.txt in dn: line."

That would mean you'd be reading your multi-gigabyte ldap.txt multiple times (i.e. once for every user in user.txt). Instead, read user.txt once and create a regex with a capture group containing an alternation of all the users. If that's unfamiliar to you, see "Perl regular expressions tutorial".

"If matches, then store the value of all the lines matching maillocaladdress to the varialbe , I assume in hash key/value pari but here the values are more than one."

What you want here is a "hash of arrays".

Putting all that together (based on your sample data):

#!/usr/bin/env perl

use strict;
use warnings;
use autodie;

my ($user_file, $ldap_file) = qw{pm_1079590_user.txt pm_1079590_ldap.t
+xt};

open my $user_fh, '<', $user_file;
my @users;
while (<$user_fh>) {
    chomp;
    push @users, $_;
}
close $user_fh;

my $user_re = 'uid=(' . join('|', @users) . '),';

my %user_ldap_data;

open my $ldap_fh, '<', $ldap_file;
my $user = '';
while (<$ldap_fh>) {
    if (/^dn:/) {
        $user = /$user_re/ ? $1 : '';
        next;
    }

    next unless $user;

    push @{$user_ldap_data{$user}}, $1 if /^maillocaladdress:\s+(\S+)/
+;
} 
close $ldap_fh;

use Data::Dump;
dd \%user_ldap_data;
[download]

Output:

{
  game  => [
             "game\@example.com",
             "game.test\@example.com",
             "game-test\@example.com",
           ],
  test1 => [
             "test1\@example.com",
             "test.team\@example.com",
             "test11\@example.com",
           ],
}
[download]