Abstract: Matrix-assisted laser desorption/ionization time-of-flight mass spectrometer (MALDI-TOF MS) plays a key role in the field of modern basic scientific research and analysis. Resolution is an important indicator to evaluate the performance of a mass spectrometer to distinguish ions with different mass-to-charge ratios. A mass spectrometer with higher resolution can provide more accurate measurement results, which is particularly important when analyzing and identifying the components in complex samples and distinguishing similar structural ions. In order to optimize the design of MALDI-TOF MS and improve the resolution of the instrument, the following steps were adopted. Firstly, the mathematical theoretical model of linear TOF MS induced by double-field acceleration delay was established by Matlab, and four possible distributions of ions in space and velocity were listed. To address the shortcomings of the Whale optimization algorithm, including slow convergence speed, low precision and susceptibility to local optima, improvements were made on the convergence factor, inertia weight and position update strategy. Subsequently, aiming at improving the resolution, the optimization and calculation of the instrument parameters were carried out. Considering that the selection of acceleration length could influence the selection of extraction length and field-free flight tube length, through comparative analysis, acceleration length is set to a fixed value of 12 mm. Then, by analyzing the distribution diagrams of extraction length and field-free flight tube length of ions under different mass-to-charge ratios at the ideal resolution, extraction length and field-free flight tube length are set to 3 mm and 0.95 m, respectively. Since the distribution of extraction length and field-free flight tube length, and the distribution of extraction voltage and delay time at the ideal resolution both showed that the curve of distribution 1 is far away from the curves of the latter three distributions, and the curve of distribution 4 is in the middle of the curves of distribution 2 and distribution 3. In order to take into account distribution 2 and distribution 3, distribution 4 are selected as the research object. Finally, the effect of extraction voltage and delay time on resolution was obtained through optimization analysis. For any ion with a relative molecular mass in the range of 2 000-20 000 u, a relatively high resolution can be obtained by selecting the optimal parameter combination of the corresponding extraction voltage and delay time under distribution 4.