In this article, the carbon fiber reinforced vinyl ester (CVE) composite was modified with pristine and functionalized carbon nanotubes (CNTs/FCNTs) using the in situ polymerization and electrophoretic deposition (EPD) techniques: individually and using both simultaneously. Their influence on the flexural properties of the composites at room (RT), cryogenic (−196°C) (CT), and elevated (70°C) (ET) temperatures were compared. Through matrix modification, the best flexural strength with CNT and FCNT modified composites was found to be 6.2% and 9.9% higher over neat CVE composite. Similarly, following the EPD technique, the optimum flexural strength enhancement with CNT and FCNT was recorded to be 10.3% and 13.8% with respect to the control composite respectively. A synergetic impact could be noticed by combining both the techniques together, where the flexural strength of the hierarchical composite with FCNT modification was improved by ~22%, ~25%, and ~ 6% higher than that of control CVE at RT, CT and ET respectively. The dispersion quality of nanotubes in the matrix and on the carbon fiber surface, and fractured surface morphology is analyzed using a SEM.