The spectra measurements mode that suitable for haploid maize kernel identification was explored using MicroNIR-1700 series of miniature near infrared spectrometer by JDSU company. Based on Near Infrared Spectroscopy (NIRS) qualitative analysis techniques, we conducted a comparative study using reflectance and transmittance spectra to identify haploid maize kernels. Partial least squares-discriminant analysis(PLS-OLDA) was used to compress the pretreated spectral data, and then the identification models were built based on Support Vector Machine (SVM). The measured data were recorded in reflectance and transmittance modes and the recognition correct rates were calculated. For measurements taken in reflectance mode, the average recognition rate was less than 60% regardless of embryo side positions. In transmittance mode, however, the average recognition rate reached 93.2%. The experiment results show that diffuse reflection spectrum could only obtain corn grain surface information, so embryo side positions severely affect haploid maize kernel identification effect when reflectance measurements mode have been employed, but they have far less impact on transmittance mode. The near infrared diffuse transmittance spectra analyzes non-uniform samples can achieve the analysis of optical path depth information accumulation, all information of the sample interior can be obtained, so transmittance spectra could identify haploid maize effectively and be desensitized to kernel positions. NIRS qualitative analysis techniques with features of rapid, nondestructive could identify the haploid and Micro-NIR spectrometer scan fast and cost less, which have utility for automatically selecting haploid maize kernels from hybrid kernels.