Herein, this work aims to directly visualize the morphological evolution of the controlled self-assembly of star-block polystyrene-block-polydimethylsiloxane (PS-b-PDMS) thin films via in situ transmission electron microscopy (TEM) observations. With an environmental chip, possessing a built-in metal wire-based microheater fabricated by the microelectromechanical system (MEMS) technique, in situ TEM observations can be conducted under low-dose conditions to investigate the development of film-spanning perpendicular cylinders in the block copolymer (BCP) thin films via a self-alignment process. Owing to the free-standing condition, a symmetric condition of the BCP thin films can be formed for thermal annealing under vacuum with neutral air surface, whereas an asymmetric condition can be formed by an air plasma treatment on one side of the thin film that creates an end-capped neutral layer. A systematic comparison of the time-resolved self-alignment process in the symmetric and asymmetric conditions can be carried out, giving comprehensive insights for the self-alignment process via the nucleation and growth mechanism.