It has been a challenge to understand the negative fouling resistance during the induction stage of many crystallization fouling processes. The evolution of complex fouling layer structure (i.e., mesoscale crystal structure) and its intricate interaction with heat and momentum transfer in a heat exchanger are extremely difficult to be rigorously tracked experimentally. In this work, a 3D computational fluid dynamics (CFD) model was developed for the induction stage of fouling in a microscale channel. The growth of crystals with artificially designed structures at the micrometer scale has been explicitly modeled and coupled with flow dynamics and heat transfer. This model offers unique opportunities to investigate a variety of crystal structures that include the density, distribution, shape, orientation, and growth schemes. Dominant mechanisms of heat transfer enhancement during the induction stage have been demonstrated by the quantification and analysis of Nusselt number ratios. Moreover, quantitative findings in this work can be used to guide the design of high-performance heat transfer facilities. (C) 2017 Elsevier Ltd. All rights reserved.