To address the problem that safe scheduling is not taken into consideration in existing multi-scientific scheduling workflow algorithm in cloud environment, this paper proposes a multi-scientific workflows security-deadline constraint cost optimization algorithm (MSW-SDCOA). First, based on data flow dependency, MSW-SDCOA compresses scientific workflow and reduces the number of task nodes to save scheduling cost. Secondly, through optimizing HEFT algorithm, a scheduling sequence is formed to realize overall multi-objective optimization scheduling. Lastly, by optimizing update strategies of pheromone and heuristic information in ant colony optimization (ACO), cost optimization effect is further improved. The simulation experiment results show that the cost optimization effect of MSW-SDCOA algorithm is about 14% better than that of MW-DBS algorithm.