The low level of physical fitness among Chinese adolescents has a negative impact on schooling and health. The weight-adjusted waist index (WWI) has attracted much attention as a novel indicator for assessing body composition. However, little research has been conducted on the association between WWI and the physical fitness index (PFI) among adolescents in the Xinjiang region of western China. A randomized whole-cluster sampling method was used to assess 4496 adolescents aged 12-17 years in Xinjiang, China. The assessment indexes included height, weight, waist circumference, grip strength, sit-up, standing long jump, sit and reach, 50 m dash, 20-mSRT, and the WWI and PFI were calculated. One-way analysis of variance (ANOVA), Kruskal Wallis rank sum test, Pearson correlation analysis, and curvilinear regression analysis were used to analyze the correlations that existed between WWI and PFI. The differences in PFI between different WWI subgroups of Chinese adolescents in Xinjiang were all statistically significant when compared with each other (H-values of 57.058, 137.515, and 19.443, P < 0.01). The analyzed results did not change according to age. Similarly, the same trend was observed for boys and girls. Overall, WWI showed an inverted "U" curve relationship with PFI, and the effect of increased WWI on PFI was more pronounced in boys than in girls. When the WWI is 8.8, the PFI is at its highest level, i.e. 0.131. The relationship between WWI and PFI in Chinese adolescents in Xinjiang showed an inverted "U" curve, with lower or higher WWI negatively affecting PFI, and the effect on boys was more obvious than that on girls. In the future, the WWI level of Chinese adolescents in Xinjiang should be effectively controlled to keep it within a reasonable range, promote the development of physical fitness, and safeguard physical and mental health.