Background: Individuals with gaming disorder (GD) exhibit autonomic nervous system responses that indicate dysfunctional emotion regulation. Pulse rate variability (PRV) is a valuable biomarker for investigating the autonomic function of patients with mental disorders. Because individuals with GD dynamically regulate emotions during gaming, the PRV response relating to GD is not well understood. To investigate the dynamic PRV responses of individuals with GD, this study proposed the indexes of instantaneous PRV (iPRV) and instantaneous respiratory frequency (IFresp) of arterial blood pressure signals using empirical mode decomposition and normalized direct-quadrature algorithms. iPRV consists of low-frequency (LF), high-frequency (HF), and very high-frequency (VHF) bands. Moreover, a novel method of extended classifier system with continuous real-coded variables (XCSR) was used to detect GD and extract GD-related iPRV features using iPRV and IFresp as input data. Results: A total of 32 college students without depressive and anxiety symptoms or cardiovascular diseases were recruited in this study. Participants were grouped into the high-risk GD and low-risk GD using both Chen Internet Addiction Scale and Internet Gaming Disorder Questionnaire. Their arterial blood pressures signals were measured while they watched gameplay videos with negative or positive emotional stimuli. Seven participants with high-risk GD exhibited significantly increased normalized VHF (nVHF) PRV and IFresp readings and significantly decreased normalized LF (nLF) PRV readings and LF/HF PRV ratios (from baseline) during negative or positive gameplay videos stimuli. These participants also exhibited higher nVHF PRV and lower nLF PRV readings and LF/HF PRV ratios when they experienced negative gameplay video stimuli relative to 17 participants with low-risk GD. The classification accuracy of the XCSR reached 90% for both negative and positive video stimuli, and nVHF PRV was most frequently used to detect GD risk. Conclusions: iPRV and IFresp can be used to detect GD and analyze the autonomic mechanism of individuals with GD.