The influence of polydispersity on the interfacial kinetics of end-coupling and microstructure formation in the melt of immiscible polymers was studied using dissipative particle dynamics simulations. The irreversible reaction started at a flat interface between two layers, each of which contained polymer chains of two different lengths with functionalized or unreactive end groups. As in the case of fully functionalized monodisperse reactants [A. V. Berezkin and Y. V. Kudryavtsev, Macromolecules 44, 112 (2011)], four kinetic regimes were observed: linear (mean field coupling at the initial interface), saturation (decreasing the reaction rate due to the copolymer brush formation or reactant depletion near the interface), autocatalytic (loss of the initial interface stability and formation of a lamellar microstructure), and terminal (microstructure ripening under diffusion control). The interfacial instability is caused by overcrowding the interface with the reaction product, and it can be kinetically suppressed by increasing chain length of the reactants. Main effects of polydispersity are as follows: (i) the overall end-coupling rate is dominated by the shortest reactive chains; (ii) the copolymer concentration at the interface causing its instability can be not the same as in the lamellas formed afterwards; (iii) mean length of the copolymer product considerably changes with conversion passing through a minimum when a microstructure is just formed.