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The dynamics of polymer-nanoparticle (NP) mixtures, which involves multiple scales and system-specific variables, has posed a long-standing challenge on its theoretical description. In this paper, we construct a microscopic theory for polymer diffusion in the mixtures based on a combination of generalized Langevin equation, mode-coupling approach, and polymer physics ideas. The parameter-free theory has an explicit expression and remains tractable on pair correlation level with system-specific equilibrium structures as input. Taking a minimal polymer-NP mixture as an example, our theory correctly captures the dependence of polymer diffusion on NP concentration and average interparticle distance. Importantly, the polymer diffusion exhibits a power law decay as the polymer length increases at dense NPs and/or long chain, which marks the emergence of entanglement-like motion. The work provides a first-principle theoretical foundation to investigate dynamic problems in diverse polymer nanocomposites., Comment: 10 pages, 6 figures