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In the past decades, regression approach was a main gene mapping method. For avoiding the QTL mapping to estimate the gene effects, the molecular marker regression was used to research the quantitative trait controlled by polygene under the condition of complete linkage between gene locus and marker. For the utilization of this method, the recombination influence on precision and accuracy estimating gene effect were researched. The results showed the recombination rate between a marker and its locus could affect the precision and accuracy estimating gene effect and allelepsilas interaction effects. The precision and accuracy were reduced along with the increasing of the recombination rate between a marker and its locus, the larger the recombination rate was, the smaller the precision and accuracy were. The precision and accuracy estimating for one gene effect and allelepsilas interaction effects could only be affected by its own recombination rate between its own marker and its locus, not by other genes recombination rate. These suggested that it was need to find a marker which was tightly or closely linked with genes for estimating the gene effect and allelepsilas interaction effects precisely, especially for a gene locus with a large allelepsilas interaction coefficient and relative gene effects.