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In this paper, we compute the correlation functions of Wilson(-'t~Hooft) loops with chiral primary operators in $\mathcal{N}=4$ supersymmetric Yang-Mills theory with $SO(N)$ gauge symmetry, which has a holographic dual description of Type IIB superstring theory on the $AdS_{5}\times\mathbf{RP}^{5}$ background.Content from this work may be used under the terms of the Creative Commons Attribution 3.0 licence. Any further distribution of this work must maintain attribution to the author(s) and the title of the work, journal citation and DOI. Article funded by SCOAP3 and published under licence by Chinese Physical Society and the Institute of High Energy Physics of the Chinese Academy of Science and the Institute of Modern Physics of the Chinese Academy of Sciences and IOP Publishing Ltd. Specifically, we compute the coefficients of the chiral primary operators in the operator product expansion of Wilson loops in the fundamental representation, Wilson-'t Hooft loops in the symmetric representation, Wilson loops in the anti-fundamental representation and the spinor representation. We also compare these results to the $\mathcal{N}=4$ $SU(N)$ super Yang-Mills theory.