One kind of “human-instrument integration” principle for designing workstations of desktop microscopic instruments which can provide better user experience is proposed in this article. The workstation based on the principle takes the operator as the center. In this way, the efficiency and comfort level are maximized, and the operating fatigue is reduced. Aiming at the operation characteristics and work path of the biological microscope, three kinds of workstation layout schemes are designed. The software Jack is used to evaluate operating time and energy consumption. The comparison experiment for operation comfort of the working postures is completed. The RMS of surface EMG for the main muscles of the neck and shoulder is tested by paired T test. The results show that the splenius capitis on the turning side and the sternocleidomastoid on the corresponding side are the most sensitive with bigger load variation, and the average RMS change rates are 56. 4% and 8. 4% respectively. Combined with the subjective evaluation of operators, the more comfortable overlapped type is finally determined as the optimal layout. The assessment method verifies the effectiveness of the “human-instrument integration” principle, which can provide guidance for the workstation design of related microscopic instruments.