Additive manufacturing (AM) can produce almost any product shape through layered stacking. The usability of continuous fiber-reinforced polymers (CFRP) fabricated by AM, however, is restricted owing to the limitations of no reinforcing fibers in the lay-up direction and weak interface bonding between the fibers and matrix. This study presents molecular dynamics in conjunction with experiments to explore how ultrasonic vibration enhances the performance of continuous carbon fiber-reinforced polylactic acid (CCFRPLA). Ultrasonic vibration improves the mobility of PLA matrix molecular chains by causing alternative fractures of chains, promoting crosslinking infiltration among polymer chains, and facilitating interactions between carbon fibers and the matrix. The increase in entanglement density and conformational changes enhanced the density of the PLA matrix and strengthened its anti-separation ability. In addition, ultrasonic vibration shortens the distance between the molecules of the fiber and matrix, improving the van der Waals force and thus promoting the interface binding energy between them, which ultimately achieves an overall improvement in the performance of CCFRPLA. The bending strength and interlaminar shear strength of the specimen treated with 20 W ultrasonic vibration reached 111.5 MPa and 10.16 MPa, respectively, 33.11% and 21.5% higher than those of the untreated specimen, consistent with the molecular dynamics simulations, and confirmed the effectiveness of ultrasonic vibration in improving the flexural and interlaminar properties of the CCFRPLA.