Alexithymia is associated with deficiencies in recognizing and expressing emotions and impaired emotion regulation, though few studies have verified the latter assertion using objective measures. This study examined startle reflex modulation by fearful imagery and its associations with heart rate variability in alexithymia. Fifty‐four adults (27 alexithymic) imagined previously normed fear scripts. Startle responses were assessed during baseline, first exposure, and reexposure. During first exposure, participants, in separate trials, engaged in either shallow or deep emotion processing, giving emphasis on descriptive or affective aspects of imagery, respectively. Resting heart rate variability was assessed during 2 min of rest prior to the experiment, with high alexithymic participants demonstrating significantly higher LF/HF (low frequency/high frequency) ratio than controls. Deep processing was associated with nonsignificantly larger and faster startle responses at first exposure for alexithymic participants. Lower LF/HF ratio, reflecting higher parasympathetic cardiac activity, predicted greater startle amplitude habituation for alexithymia but lower habituation for controls. Results suggest that, when exposed to prolonged threat, alexithymics may adjust poorly, showing a smaller initial defensive response but slower habituation. This pattern seems related to their low emotion regulation ability as indexed by heart rate variability.