The effect of surface chemical heterogeneity and hydrodynamics on particle transport and deposition in porous media was investigated by microscale simulations using a colloidal particle tracking model, called 3D-PTPO (Three-dimensional particle tracking model by Python® and OpenFOAM®) code. This work is aimed as a step toward modeling of transport and deposition in porous media idealized as a bundle of straight capillary tubes. Therefore, our focus is put upon a three-dimensional capillary with periodically repeating chemically heterogeneous surfaces namely crosswise strips patterned and chess board patterned. The main feature of this recent model is to renew the flow field by reconstructing the pore structure, to take the pore surface modification induced by the volume of the deposited particles into account. The dependency of the deposition probability and the dimensionless surface coverage (Γ/ΓRSA) on the frequency of the pitches (λ), the Péclet number (Pe) and the favorable area fraction (θ), as well as the distribution of the spatial density of deposited particles along the capillary tube were studied. The results indicate that particles tend to deposit at the leading and trailing edges of the favorable strips, and the deposition is more uniform along the patterned capillary compared to the homogeneous one. In addition, for the chemically heterogeneous capillary, in a similar manner as for the homogeneous one, a definite plateau exists for the Γ/ΓRSA at low Péclet values. For high Pe values, the declining trend for Γ/ΓRSA versus Pe is in good agreement with the derived power law dependence already observed in the literature for fully adsorbing surfaces. Moreover, for fixed θ the deposition probability is linearly correlated with λ and for given λ, such a deposition probability is also a linear function of θ.< Réduire