The Barcelona star took his total for the country to 35 from 82 caps, one more than the iconic World Cup winner.
The 25-year-old, who has this week protested his innocence amid reports the Spanish tax authorities are investigating allegations of fraud against him and his father, is now level in second place in the scoring charts with Hernan Crespo, still 21 behind Gabriel Batistuta.
"Messi will keep on breaking records," Argentina coach Alejandro Sabella said on the Argentinian Football Association website.
Messi said: "The attitude of the group was very good and the team took the match seriously.
"We are preparing for the World Cup and we have been doing all the right things. The idea was to build a strong team and, slowly, we are getting there."
Messi played for 67 minutes, opening the scoring 13 minutes in.
Augusto Fernandez made it 2-0 before the Barcelona forward scored from the penalty spot before completing his hat-trick after the break.
Messi and Sergio Aguero were the only regular starters to play from the beginning, but the visitors still dominated.
Argentina created chances from the start with Ezequiel Lavezzi, Aguero and Messi all going close before the latter netted his first with a shot from outside the box.
Guatemala showed little ambition in a game which looked a lot like a training session, Fernandez doubling the advantage in the 34th minute with a header.
Five minutes later Messi was fouled in the box and he made the hosts pay from the spot with his second goal.
For the second half Sabella brought on Roma's Erik Lamela for his debut as Aguero was withdrawn.
Two minutes after the break a fine team move ended when Lavezzi crossed for Messi to complete the scoring.
The crowd spent much of the second half calling on the Argentina players to pass to Messi and the game went flat when he was substituted.
Guatemala's only chance came in injury time with a shot from long range.