Phatlum got off to a flying start as she birdied her first three holes and picked up further shots at seven and nine to reach the turn in 31.
Birdies at 11 and 13 suggested the Thai was going to establish a commanding lead but a bogey at 14 slowed her momentum and she finished with a six-under-par 66.
That handed the 23-year-old a one-shot advantage over South Korea's Amy Yang who had also got off to an impressive start and was four under after six holes.
She would pick up further birdies on 11 and 18 but a dropped shot on 15 left her just one stroke ahead of an intimidating group at four under.
World number one Inbee Park, world number five So-yeon Ryu and former LPGA Championship winner Anna Nordqvist all fired 68s at Guadalajara Country Club and will be looking to make a move on Friday.
Michelle Wie led the American challenge on three under alongside another South Korean in Jenny Shin.
Defending champion Christie Kerr endured a nightmare day as she birdied the second but then dropped six shots to sit in last place on five over.
Scotland's Catriona Matthew fired a 74 and was eight shots off the lead while England's Jodi Ewart Shadoff was a further shot back.