Single cell RNA sequencing (scRNA-seq) allows quantitative measurement and comparison of gene expression at the resolution of single cells. Ignoring the batch effects and zero inflation of scRNA-seq data, many proposed differentially expressed (DE) methods might generate bias. We propose a method, single cell mixed model score tests (scMMSTs), to efficiently identify DE genes of scRNA-seq data with batch effects using the generalized linear mixed model (GLMM). scMMSTs treat the batch effect as a random effect. For zero inflation, scMMSTs use a weighting strategy to calculate observational weights for counts independently under zero-inflated and zero-truncated distributions. Counts data with calculated weights were subsequently analyzed using weighted GLMMs. The theoretical null distributions of the score statistics were constructed by mixed Chi-square distributions. Intensive simulations and two real datasets were used to compare edgeR-zinbwave, DESeq2-zinbwave, and scMMSTs. Our study demonstrates that scMMSTs, as supplement to standard methods, are advantageous to define DE genes of zero-inflated scRNA-seq data with batch effects.