Iterating through the first hash and looking for keys that exist in the two other is enough.

use strict;
use warnings;
use Data::Dump 'pp';

my %h1 = (
    a => 1,
    b => 2,
    c => 3,
);

my %h2 = (
    a => 4,
    b => 5,
    d => 10,
);

my %h3 = (
    x => 20,
    p => 15,
    b => 6,
    a => 12,

);

my %out;

for my $key (keys %h1)
{
  next unless exists $h2{$key} and exists $h3{$key};
  $out{$key} = [ $h1{$key}, $h2{$key}, $h3{$key} ];
}

pp \%out;
__END__
{ a => [1, 4, 12], b => [2, 5, 6] }
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But seeing the size of the input hashes, I'd say it might be better to do that while constructing the hashes (eg, first build %h1, then iterate through the values of %h2 but only insert the keys that already exist in %h1, and then the same for %h3), if they aren't tied hashes in the first place.