Having announced last week he will leave Liverpool when his deal expires over the summer, Alexander-Arnold was jeered when he came on in the second-half of their 2-2 draw with Arsenal.
Owen, who left Liverpool for Real Madrid during his career, said on BBC Sport: "For his own people to boo him, it's a big lump in your throat.
"I remember sitting in the players' lounge after playing against Liverpool for Newcastle, parents, myself, all in floods of tears because I'd just been booed by my own people - and I struggle to comprehend it nowadays.
"I'm probably the closest person on the planet who knows exactly what it feels like to be in Trent's shoes now. He'll be mortified."
