1 Screening time
“I love you 3000” may have various meanings. If you count the screening time of all the Marvel superheroes movies from the first “Iron man”, then it will turn out to be 3000 minutes.
2 Big number for a 5 year old
Avengers: Endgame's most iconic line wasn't even in the script. The basic meaning behind the phrase is simply just Morgan expressing how much she loves her dad. Like, 3000 is a big number for a 5-year-old kid. Some fans have interpreted it as a child-genius response to Tony's "I love you tons" comment
3 From the song “I Love You 3000”
It might also be from the song I Love You 3000. Viral, so many upon many of us have heard it. A beautiful song penned by one with an equally beautiful and apt middle name, Poetry, although she did admit to getting some help from RhymeZone for this one. Some speculators have wondered since she’s a young woman, is she an extremely forward-thinking person who anticipates the day when she and her man will be able to achieve bodily immortality as a precipitate of scientific advances?
And that she picked the year 3000 to represent a time that is way way off, sort of to say, “We will live to see that day and be together, till then and beyond.“
4 Sign of great love
“I love you 3000” may also essentially mean “I love you a lot”. It came from Avengers: Endgame. Tony Stark tucks his daughter into bed and she tells him that she loves him 3000. It was originally something that Robert Downey, Jr.'s actual kid told him and he wanted it incorporated into his (potentially) final MARVEL movie.
Tony Stark’s personal story with his kid is also said to be one of the origins of this phrase in the movie. (See Why Loki is so popular (MARVEL)?)