Both phototherapy via photocatalysts and physical puncture by artificial nanostructures are promising substitutes for antibiotics when treating drug-resistant bacterial infectious diseases. However, the photodynamic therapeutic efficacy of photocatalysts is seriously restricted by the rapid recombination of photogenerated electron–hole pairs. Meanwhile, the nanostructures of physical puncture are limited to two-dimensional (2D) platforms, and they cannot be fully used yet. Thus, this research developed a synergistic system of Ag
3
PO
4
nanoparticles (NPs), decorated with black urchin-like defective TiO
2
(BU–TiO
2-X
/Ag
3
PO
4
). These NPs had a decreased bandgap compared to BU-TiO
2-X
, and BU-TiO
2-X
/Ag
3
PO
4
(3:1) exhibited the lowest bandgap and the highest separation efficiency for photogenerated electron–hole pairs. After combination with BU-TiO
2-X
, the photostability of Ag
3
PO
4
improved because the oxygen vacancy of BU-TiO
2-X
retards the reduction of Ag
+
in Ag
3
PO
4
into Ag
0
, thus reducing its toxicity. In addition, the nanospikes on the surface of BU-TiO
2-X
can, from all directions, physically puncture bacterial cells, thus assisting the hybrid's photodynamic therapeutic effects, alongside the small amount of Ag
+
released from Ag
3
PO
4
. This achieves synergy, endowing the hybrid with high antibacterial efficacy of 99.76 ± 0.15% and 99.85 ± 0.09% against
Escherichia coli
and
Staphylococcus aureus
, respectively, after light irradiation for 20 min followed by darkness for 12 h. It is anticipated that these findings may bring new insight for developing synergistic treatment strategies against bacterial infectious diseases or pathogenic bacterial polluted environments.