Anomalies in nuclear morphology have been linked to aging-related diseases and malignant transformation, although the mechanism responsible for this connection remains unclear. By expressing dominant-negative TER94 (TER94K2A) mutants in Drosophila photoreceptors, we show disruption of VCP (valosin-containing protein, TER94 ortholog in human), an AAA (ATPase associated with various cellular activities) ATPase essential for ubiquitin-dependent segregation or degradation of proteins, causes an age-dependent nuclear size increase. Loss of VCP function leads to accumulations of MDC1 (mediator of DNA damage checkpoint protein 1), a key DNA damage response gene, and increased γH2AV (an indicator of DNA damage), linking excessive DNA damages and associated responses to this enlarged nuclei defect. Indeed, MDC1-overexpression, similar to TER94K2A, increases γH2AV staining and nuclear size. Moreover, TER94 negatively influences MDC1 level and could interact with MDC1, suggesting that MDC1 is a VCP substrate. MDC1 accumulation increases p53 stability, and this VCP-MDC1-p53 connection is functional, as removal of p53 function suppresses the ability of TER94K2A and MDC1 overexpression to increase nuclear size. While p53 is capable of generating multiple isoforms, our genetic evidence suggests that the p53A isoform specifically contributes to this TER94K2A-associated nuclear size increase. Combining our results with a previous report that p53A expression disrupts autophagic flux, we propose that the failure of removing MDC1 in TER94K2A-expressing cells stabilizes p53A, which blocks autophagy and likely hinders the removal of nuclear content, resulting in aberrant nuclear size increase.