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The structural properties of lattice-matched InAlAs/InP layers grown by molecular beam epitaxy have been studied using atomic force microscopy, scanning electron microscopy and micro-photoluminescence spectroscopy. The formation of the surface pits with lateral sizes in the micron range and a depth of about 2 ÷ 10 nm has been detected. The InP substrate annealing temperature and value of InAlAs alloy composition deviation from the lattice-matched InxAl1−xAs/InP case (x = 0.52) control the density of pits ranging from 5 × 105 cm−2 ÷ 108 cm−2. The pit sizes are controlled by the InAlAs layer thickness and growth temperature. The correlation between the surface pits and threading dislocations has been detected. Moreover, the InAlAs surface is characterized by composition inhomogeneity with a magnitude of 0.7% with the cluster lateral sizes and density close to these parameters for surface pits. The experimental data allow us to suggest a model where the formation of surface pits and composition clusters is caused by the influence of a local strain field in the threading dislocation core vicinity on In adatoms incorporating kinetic.