Microphase separated block copolymers (BCPs) are emerging as promising templates and scaffolds for the fabrication of nanostructured materials. To achieve the desired nanostructures, it is necessary to establish convenient approaches to control the morphology of BCPs. It remains challenging to induce morphological transitions of BCPs via external fields. Click chemistry, especially alkyne/azide click chemistry, has been widely used to synthesize novel functionalized materials. Here, we demonstrate that alkyne/azide click chemistry can be used as an efficient approach to chemically modify BCPs and therefore induce morphological transitions. Alkyne-functionalized diblock copolymers (di-BCPs) poly(ethylene oxide)- block -poly(n-butyl methacrylate-random -propargyl methacrylate) (PEO-b -P(nBMA-r -PgMA)) have been successfully synthesized. When the di-BCP is blended with an azide additive Rhodamine B azide and annealed at elevated temperatures, click reaction occurs between the two components. With the Rhodamine B structure attached to the polymer backbone, the di-BCP shows dramatic change in the interactions between the two blocks and the volume fraction of each block. As a result, morphological transitions, such as disorder-to-order transitions (DOTs) and order-to-order transitions (OOTs), are observed. The reaction kinetics and morphology evolution during the click chemistry induced DOTs have been investigated by in-situ and ex-situ characterizations, and fast kinetics properties are observed. Microphase separated morphologies after the DOTs or OOTs are dictated by the composition of neat di-BCPs and the mole ratio between the alkyne and azide groups. The DOTs of PEO-b -P(nBMA-r -PgMA) di-BCPs induced by alkyne/azide click chemistry have also been achieved in thin film geometries, with comparable kinetics to bulk samples. The orientation of the microdomains is dependent on the grafting density of Rhodamine B structure as well as film thickness. At higher grafting densities, a perpendicular orientation of the microdomains can be obtained. For di-BCPs with certain compositions, the microphase separated morphologies in thin films deviate from the corresponding bulk morphologies, which is probably due to the interfacial interactions and confined geometries arising from film thickness.