Macedonia has set a deadline of September 30 for the referendum on both membership bids and a deal with Greece to change its name to the Republic of North Macedonia.
Following a meeting with Macedonian Prime Minister Zoran Zaev in the capital of Skopje on Saturday, Ms Merkel said the two issues were “very closely linked”.
She told reporters: “Without a solution to this name question, the other two things can’t happen.”
Mr Zaev said Ms Merkel’s visit to the Macedonian capital sent “a strong message and encouragement” to the country’s people ahead of the referendum “to decide their future”.
She said: “The future could be, with a successful outcome of the referendum, that you are both member of NATO as well as belonging to the family of EU states.”
In June, Macedonia was invited by NATO to begin talks over the alliance but warned this could not happen without changing its constitution and adopting the new name first.
The EU is also set to announce a date for when Macedonian accession talks will begin, pending implementation of the name deal.
Since being elected last year, Mr Zaev’s government has pushed for an agreement with Greece, with the two sides agreeing in a new name in June.
But a number of Macedonian nationalists, including President Gjorge Ivanov, have opposed the deal, claiming it goes against the constitution.
The German Chancellor’s visit to Macedonia comes exactly 27 years after the country declared independence from the former Yugoslavia.
Mr Zaev’s government will need a two-third majority in Parliament in order to implement the constitutional changes.
But it would be more difficult for the government to win this majority if the agreement with Greece is rejected in the referendum.
Recent opinion pools have shown that more than half of the country’s people are likely to vote, with most supporting the membership bids and the name deal.
In June, a Bundestag source revealed that Germany would back Albania and Macedonia’s bids to start accession talks to join the European Union.
In February, European Commission President Jean-Claude Juncker said Macedonia had “made great progress” in confronting the issues that prevented the nation joining the EU, such as its 27-year-old dispute with member state Greece, but it was not there yet.
However, the Commission proposed starting accession talks for both Macedonia and Albania as the bloc looked to widen its influence.
A German government source told politics website Politico: “Both countries have made remarkable efforts in recent years to move closer to the EU.”
However, the source added there was “still a way to go for both Albania and Macedonia”.