Objective: To evaluate certain neurophysiological parameters of basketball players, analyze the effects of aerobic and anaerobic training, and assess the role of nutrition and physical recovery. Methods: Seven male professional players (aged 19–25) from the Erdenet Miners team completed a two-month integrated intervention combining structured aerobic/anaerobic training, individualized nutrition plans, and recovery modalities. Assessments were conducted at baseline, mid-intervention, and post-intervention, measuring body composition, aerobic capacity, muscular strength, agility, pulmonary function, neuromuscular balance, and psychological recovery. Non-parametric tests (Friedman and Wilcoxon) were used to evaluate changes over time. Results: Significant improvements were observed across multiple domains. Body fat decreased from 21.6% to 19.6%, while muscle mass and protein levels increased. Aerobic capacity improved, including Cooper test performance (2.86 km to 3.22 km), Yo-Yo IR1 (1005 m to 1385 m), and MVV (156.2 to 184.9 L/min). Agility increased by 14%, vertical jump height by 6.1%, and muscular asymmetry declined. Psychological recovery (RestQ-Sport) also improved. Conclusions: A comprehensive neurophysiological intervention combining structured training, targeted nutrition, and advanced recovery techniques significantly enhanced physical performance, physiological efficiency, and psychological well-being in elite basketball players. These findings highlight the value of integrated performance-optimization strategies in improving individual and team outcomes.