Nanoplastics (NPs) pose potential ecological and health impacts. While previous studies have highlighted inconsistent toxicity levels of NPs, knowledge remains limited about the specific effects of different NPs on embryonic development, early life-stage behaviors, and bodily uptake. This study examines the effects of polystyrene NPs (PS-NPs) with different surface charges, plain polystyrene (PS), amino-modified (PS-NH2), and carboxyl-modified (PS-COOH) on zebrafish early life stages. High-resolution 3D bioimaging confirmed differential internalization: PS-COOH accumulated in the yolk and intestine, while PS-NH2 localized mainly in the intestine. PS-NPs up to 10 ppm did not significantly affect mortality or hatching rates, likely due to effective dialysis, minimizing toxic chemical leaching. PS-NP exposure led to noninflated swim bladders and affected swimming. RNA sequencing identified impacted neurological molecular pathways like circadian rhythm and visual function; weighted gene coexpression network analysis indicated strong correlations between key gene modules and phenotypic traits like eye development and dopamine level. We highlight the low acute toxicity of clean dialyzed NPs despite bodily uptake and surface-charge-dependent sublethal neurotoxicity. Overall, plain PS-NPs induced significant individual-level effects, while charged PS-NPs caused stronger molecular-level alterations; toxicity profiles varied across biological levels, complicating hazard assessment and underscoring the need for population-level studies on ecological impacts.