Localizing electrical sources on the cortex surface from scalp recorded electroencephalogram (EEG) is challenging, due to ill-posed problem, noises/artifacts contamination, etc. Applying sparse Bayesian learning (SBL) in this field can automatically give sparse solution to ill-posed problem, while most of the SBL-based algorithms require precise or estimated version of noise statistics information. As EEG signals are more likely to stem from locally synchronized neural masses, modeling source block-sparsity on the cortex surface would bring benefits. In this paper, we develop an EEG brain source localization algorithm in SBL framework, with innovative modeling at sensor level as well as source level. For sensor-level modeling, the distribution of sample covariance matrix of multi-electrode measurements is considered, to circumvent the requirement of noise covariance matrix information. The innovation of source-level modeling is that, with block-sparsity prior used, the block-sparse signal reconstruction problem is transformed to an atom-sparse one, in which variance parameters of brain regions are to be estimated. As these parameters are nonnegative, their priors are modeled by nonnegative Gaussian, which was neglected by previous studies, and ultimately a nonnegative block-SBL (NNBSBL) algorithm is proposed in expectation–maximization (EM) approach. Simulations demonstrate that the proposed NNBSBL algorithm has excellent performance in variations of source number, source locations, homoscedastic/heteroscedastic noises, signal-to-noise ratio (SNR), and number of samples, compared to benchmark and state-of-the-art algorithms. The performance of the proposed algorithm is also evaluated through real P300 EEG data, which is proved consistent with the conclusions of P300 source locations in literature.