Zinc (Zn) deficiency reduces chlorophyll content and damages chloroplast structure in leaves. However, little is known about the responses of chlorophyll synthesis and chloroplast structure of plants to Zn deficiency stress at the transcriptomic and proteomic level. In the present study, maize seedlings of cultivar ZD958 were grown in nutrient solution with 0 and 1.0 μmol·L Zn treatments. Zn deficiency stress reduced photosynthetic rate at 10 and 15 days after treatment (DAT) and the chlorophyll content (SPAD value) at 15 DAT. Eight differentially expressed genes and 6 differential abundance proteins were involved in chlorophyll biosynthetic process in Zn deficient leaves. Genes related with the key enzymes catalyzing the chlorophyll synthesis including magnesium-chelatase subunit ChlH chloroplastic, magnesium protoporphyrin IX methyltransferase chloroplastic showed down-regulated trend by Zn deficiency at the transcriptome or proteome levels. The defective chloroplast structure of Zn-deficient leaves showed less grana granule and loose membrane. Seven changed genes in transcriptome profile were assigned to thylakoid membrane organization in Zn-deficient leaves while 8 differential abundance proteins in proteome data. The expression of the genes related with thylakoid membrane organization process such as protein PHOTOSYSTEM I ASSEMBLY 2, chloroplastic were down-regulated under limited Zn deficiency at both transcriptome and proteome levels.