Watkins was omitted from the latest Three Lions squad - the last before Thomas Tuchel makes his selection for the tournament - following a difficult season at club level.
But Emery has told the 30-year-old there is still time for him to force his way back into the picture with a strong finish to the campaign.
Watkins has scored twice in Villa’s last four matches after failing to find the net in seven.
Emery said: “Maybe he can feel a bit disappointed.
“But keep going. He was not involved with the national team three years ago. Then, he was involved for two years and now he is not.
“But if he is playing like Sunday, again, he is going to have chances to come back.”
Watkins is still on course to be Villa’s top scorer for the sixth straight season, after netting his 10th goal in all competitions in last weekend’s Premier League over West Ham.
The former Brentford man scored the most memorable goal of his England career at Euro 2024, when he scored a last-gasp semi-final winner against the Netherlands.
But he risks missing out on World Cup selection for the second straight tournament due to an untimely loss of form.
Watkins saw his career revived by Emery’s arrival after he was omitted from the 2022 squad.
Asked about his latest setback, the striker said: “Everyone wants to play for their country but I expected (to be left out) because my form has not been that great.
“I know what I can do and when I put on an England shirt I feel like I have always performed well.”