Understanding brain function represents a fundamental goal in neuroscience, with critical implications for therapeutic interventions and neural engineering applications. Computational modeling provides a quantitative framework for accelerating this understanding, but faces a fundamental trade-off between computational efficiency and high-fidelity modeling. To address this limitation, we introduce a novel Energy-based Autoregressive Generation (EAG) framework that employs an energy-based transformer learning temporal dynamics in latent space through strictly proper scoring rules, enabling efficient generation with realistic population and single-neuron spiking statistics. Evaluation on synthetic Lorenz datasets and two Neural Latents Benchmark datasets (MC_Maze and Area2_bump) demonstrates that EAG achieves state-of-the-art generation quality with substantial computational efficiency improvements, particularly over diffusion-based methods. Beyond optimal performance, conditional generation applications show two capabilities: generalizing to unseen behavioral contexts and improving motor brain-computer interface decoding accuracy using synthetic neural data. These results demonstrate the effectiveness of energy-based modeling for neural population dynamics with applications in neuroscience research and neural engineering. Code is available at https://github.com/NinglingGe/Energy-based-Autoregressive-Generation-for-Neural-Population-Dynamics.