Waxy corn is a special type of maize primarily consumed as a fresh vegetable by humans. Nitrogen (N) plays an essential role in regulating the growth progression, maturation, yield, and quality of waxy maize. A reasonable N application rate is vital for boosting the accumulation of both N and carbon (C) in the grains, thereby synergistically enhancing the grain quality. However, the impact of varying N levels on the dynamic changes in N metabolism, carbohydrate formation, and anthocyanin synthesis in purple waxy corn kernels, as well as the regulatory relationships among these processes, remains unclear. To explore the effects of varying N application rates on the N metabolism, carbohydrate formation, and anthocyanin synthesis in kernels during grain filling, a two-year field experiment was carried out using the purple waxy maize variety Jinnuo20 (JN20). This study examined the different N levels, specifically 0 (N0), 120 (N1), 240 (N2), and 360 (N3) kg N ha. The results of the analysis revealed that, for nearly all traits measured, the N application rate of N2 was the most suitable. Compared to the N0 treatment, the accumulation and content of anthocyanins, total nitrogen, soluble sugars, amylopectin, and C/N ratio in grains increased by an average of 35.62%, 11.49%, 12.84%, 23.74%, 13.00%, and 1.87% under N2 treatment over five filling stages within two years, respectively, while the harmful compound nitrite content only increased by an average of 30.2%. Correspondingly, the activities of related enzymes also significantly increased and were maintained under N2 treatment compared to N0 treatment. Regression and correlation analysis results revealed that the amount of anthocyanin accumulation was highly positively correlated with the activities of phenylalanine ammonia-lyase (PAL) and flavanone 3-hydroxylase (F3H), but negatively correlated with anthocyanidin synthase (ANS) and UDP-glycose: flavonoid-3-O-glycosyltransferase (UFGT) activity, nitrate reductase (NR), and glutamine synthetase (GS) showed significant positive correlations with the total nitrogen content and lysine content, and a significant negative correlation with nitrite, while soluble sugars were negatively with ADP-glucose pyrophosphorylase (AGPase) activity, and amylopectin content was positively correlated with the activities of soluble starch synthase (SSS), starch branching enzyme (SBE), and starch debranching enzyme (SDBE), respectively. Furthermore, there were positive or negative correlations among the detected traits. Hence, a reasonable N application rate improves purple waxy corn kernel nutritional quality by regulating N metabolism, as well as carbohydrate and anthocyanin biosynthesis.