The company said visitor numbers were still 'significantly' down at Alton Towers and revenues across the theme parks business, which includes Thorpe Park and Warwick Castle, was down seven per cent to £104m.
But new international theme parks opening in Shanghai, Michigan and Arizona helped boost the overall performance of the business, which has 111 sites worldwide.
As a result group pre-tax profits for the first half of Merlin's year edged by £1m to £50m, while revenue was up 5.3 per cent to £573m.
The company will be sentenced later this year in connection with the Smiler rollercoaster crash which left five people seriously injured.
Merlin has already admitted a breach of health and safety rules over the incident in June last year, which left two young women needing leg amputations when their carriage hit another stationary car.
The company is expected to receive a hefty fine following the two-day hearing at Stafford Crown Court in September.
But the company's upcoming court case was absent from the latest update from chief executive Nick Varney, as Merlin copes with a 'challenging' market in London and at Alton Towers as well as growing security worries following a string of terror attacks in Europe.
Mr Varney said: "Merlin has delivered a resilient performance in the first half that reflects the benefit of our diversified portfolio and strong new business development programme.
As previously reported, many of the trends we experienced last year continued into 2016.
Our Midway Attractions operating group has continued to see a challenging market in London, and Alton Towers, whilst seeing some recovery in mainstream leisure visitation, continues to experience significantly lower overall volumes.
"By contrast, and following two years of exceptional growth, our Legoland Parks operating group has continued to build on its strong performance. However, 2016 has also brought some new challenges.
Heightened security concerns, following attacks across Europe, have had an effect on city centre tourism, creating a challenging market and compounding an already difficult market in London."
But he said Merlin expected a continue recovery for its Resort Theme Parks and said there could be a further potential boost from three new Lego movies expected over the next three years.
And the weakness of the pound could make the UK tourist market more attractive to international visitors.
Merlin has opened its first Chinese theme park in Shanghai, while new attractions include the first virtual reality ride, Galactica, at Alton Towers.
And Merlin is adding 2,000 new hotel rooms across its estate, including a 76-room 'CBeebies Land' hotel to open at Alton Towers next year.