Matthew Belmonte's research asks how domain-general cognitive capacities shape the developmental emergence of both social and non-social perception, cognition and action — giving rise to individual differences therein and autistic disorders thereof. Using both cognitive neuroimaging (EEG/ERP and fMRI) and behavioural methods, Belmonte enunciated the now widely accepted and supported theory of dysconnectivity within and between autistic neural and cognitive networks, in which differences of local neural network entropy perturb activity-dependent development of long-range network connectivity, impairing top-down integrative control and enhancing autonomous processing. A current clinical application of this work assays the effect of computer-assisted training of prerequisite motor skills on autistic social communicative ability, whilst work in basic science is exploring interactions of autistic traits, cognitive sex differences, individualistic versus collectivistic cultures, and situational manipulations of psychological distance and level of construal.

Belmonte served on the Scientific Review Council of Cure Autism Now (2000 - 2006), was a founding member of the editorial board of Autism Research, the journal of the International Society for Autism Research (2007 - 2015), and since 2009 has served on the editorial boards of Molecular Autism and of Frontiers in Evolutionary Psychology and Neuroscience. He has been an ad hoc reviewer for 47 other journals, as well as for the UK Medical Research Council, UK Economic and Social Research Council, US National Institutes of Health, US National Science Foundation, US Army Congressionally Directed Medical Research Programs, Netherlands Organisation for Scientific Research, Hungarian Scientific Research Fund, Autism Speaks, and several other foundations and institutions.

Belmonte's work has been cited more than four thousand times, and funded to a total of more than £910,000 by governmental and private sponsors including the US National Science Foundation, the US-India Educational Foundation, Autism Speaks, Cure Autism Now, Fundacão Bial, and Santander. He maintains active collaborations in India and the United Kingdom. He was the recipient of the 2010 Neil O'Connor Award from the British Psychological Society (Developmental Psychology Section).