The process of generating type I/II collagen scaffolds is fraught with bubble formation, which can interfere with the three-dimensional structure of the scaffold. Herein, we applied low-temperature vacuum freeze-drying to remove mixed air bubbles under negative pressure. Type I and II rubber sponges were acid-solubilized via acid lysis and enzymolysis. Thereafter, vacuum negative pressure was applied to remove bubbles, and the cover glass press method was applied to shape the type I/II original scaffold. Vacuum negative pressure was applied for a second time to remove any residual bubbles. Subsequent application of carbamide/N-hydroxysuccinimide cross-linked the scaffold. The traditional method was used as the control group. The structure and number of residual bubbles and pore sizes of the two scaffolds were compared. Based on the relationship between the pressure and the number of residual bubbles, a curve was created, and the time of ice formation was calculated. The bubble content of the experimental group was significantly lower than that of the control group (P < 0.05). The pore diameter of the type I/II collagen scaffold was higher in the experimental group than in the control group. The time of icing effect of type I and II collagen solution was 136.54 ± 5.26 and 144.40 ± 6.45s, respectively. The experimental scaffold had a more regular structure with actively proliferating chondrocytes that possessed adherent pseudopodia. The findings indicated that the vacuum negative pressure method did not affect the physical or chemical properties of collagen, and these scaffolds exhibited good biocompatibility with chondrocytes.