In the present study, we have developed a mathematic model describing quasi-continuous catalytic synthesis of multi-walled carbon nanotubes (MWCNTs) in a fluidized bed (FB) reactor. The special attention has been paid to the effects related to heat release or absorption during MWCNT synthesis. The heat of the reaction for MWCNT growth has been shown to significantly affect the thermal field in the reactor with the diameter as low as 6 cm. We attribute this to the extremely low thermal conductivity of aerogel-like MWCNT agglomerates (0.5–0.7 W/(m·K)), the basic units of the fluidized bed. According to the proposed model, the overheating up to 60 degrees takes place in the reactor with the diameter of D = 18 cm, the wall temperature of 943 K, and blown by 1:1 C2H4/Ar mixture. We have observed major changes caused by overheating: the activity of the catalyst and morphological properties of the produced MWCNTs (outer diameter, the structure of the walls, and fraction of impurities). The role of these thermal effects rises dramatically with increasing the reactor size and should be taken into account when designing reactors for large-scale production of MWCNTs.