This meta-analysis was conducted to study whether kinematically aligned total knee arthroplasty (TKA) improves short-term functional outcomes compared with mechanical alignment without changing the hip-knee-ankle angle. Prospective cohort studies were searched from electronic literature databases, including PubMed, Web of Science, Embase (Ovid interface), and Cochrane Library (Ovid interface). Total 1,159 records were identified. Six trials involving 561 patients were eligible for data extraction and meta-analysis. The included studies recorded outcomes in the follow-up range from 6 to 34 months. Primary outcomes were to assess the functional outcomes in follow-up, and KA group achieved better performance on WOMAC score (mean difference [MD] = -18.82, 95% CI: -16.06 to -5.58), knee function score (MD = 7.23, 95% CI: 0.52-13.94), Oxford knee score (MD = 4.76, 95% CI: 0.40-9.12), and knee range of flexion (MD = 4.48, 95% CI: 2.09-6.86), whereas other parameters including Knee Society score, knee range of extension, VAS pain score, and the occurrence of the complications were without significant difference (p > 0.05). Second outcomes evaluated the perioperative clinic indexes. Our meta-analysis showed that KA group had a shorter time of operation (MD = -15.44, 95% CI: -27.47 to -3.71) and a longer walk distance before discharge (MD = 53.24, 95% CI: 21.32-85.15) when compared with the MA group, whereas the change in hemoglobin, incision length, knee range of flexion before discharge, and length of stays were without significant difference (p > 0.05). Third outcomes were used to analyze the alignment data. Our study showed that KA had larger angles of femoral component and mechanical axis of the femur (MD = -1.95,95% CI: -2.77 to -1.13), tibial component and mechanical axis of tibia (MD = 2.06, 95% CI: 1.43-2.70), anatomic knee angle (MD = -0.72, 95% CI: -1.33 to -0.11), and operative limb alignment (MD = -1.97, 95% CI: -2.50 to -1.45,) compared with the MA group, but the hip-knee-ankle angles between the two groups were similar. KA provided better functional outcomes and better flexion following short-term follow-up of TKA. However, longer-term follow-up and larger sample studies are needed to put into research in the future.