It's always preferred to use core modules, but in this case, as opposed to the OP's sub, you'd have to create a new object per conversion (if my brief overview of the module has me understand it correctly):

use warnings;
use strict;

use Benchmark qw(cmpthese);
use Time::Seconds;

my $time = '12345678';

cmpthese(1000000, {
    sub => "parse_duration('$time')",
    mod => "time_seconds('$time')",
});

sub parse_duration {
  my $seconds = shift;
  my $hours = int( $seconds / (60*60) );
  my $mins = ( $seconds / 60 ) % 60;
  my $secs = $seconds % 60;
  return sprintf("%02d:%02d:%02d", $hours,$mins,$secs);
}
sub time_seconds {
    my $seconds = shift;
    my $t = Time::Seconds->new($seconds);
    return $t->pretty;
}
[download]

Sometimes it's best just to keep it local:

        Rate   mod   sub
mod  17819/s    --  -95%
sub 373134/s 1994%    --
[download]

kudos for the other day on the quoting of the var in my own bench, fwiw ;)