Hehner's main research area is formal methods of software design. His method, initially called predicative programming, later called Practical Theory of Programming, is to consider each specification to be a binary (boolean) expression, and each programming construct to be a binary expression specifying the effect of executing the programming construct. Refinement is just implication. This is the simplest formal method, and the most general, applying to sequential, parallel, stand-alone, communicating, terminating, nonterminating, natural-time, real-time, deterministic, and probabilistic programs, and includes time and space bounds. This idea has influenced other computer science researchers, including Tony Hoare.
Hehner's other research areas include probabilistic programming, unified algebra, and high-level circuit design. In 1979, Hehner invented a generalization of radix complement called quote notation, which is a representation of the rational numbers that allows easier arithmetic and precludes roundoff error.