Malaria infection poses a great threaten to public health even nowadays. The conventional diagnosis tools of malaria parasites and vectors require systematic training for the observers accompanied by the low throughput. In this study, a new detection system, i.e., multiplex microfluidic loop-mediated isothermal amplification (m mu LAMP) array, was developed to provide a convenient, rapid and economical detection system for malaria diagnosis. A microfluidic-based detection chip was designed and developed, targeting the conserved gene of four Anopheles and two Plasmodium species responsible for most of the malaria cases occurred in China. The DNA preparation of Anopheles and Plasmodium samples was realized by using a newly-developed DNA extraction method. For this m mu LAMP array system, the detection limit was determined to be 1 pg of targeting DNA with high sensitivity (>95%) and specificity (100%). Further, the accuracy of such m mu LAMP analysis was evaluated by the analysis of 48 Anopheles mosquito samples, of which 30 were termed to be target Anopheles, displaying high consistency with that by morphological analysis. In conclusion, the m mu LAMP detection system was proved to be a visible, sensitive, specific and high-throughput diagnostic tool. Considering the portable manipulation of such detection system, our studies shed light on its potential application of malaria surveillance on the spot.