Innovation consists of making collaborative efforts in term of relationship with other organization and institutions to attain competitive advantage by means of innovative services and products, as well as different relationships with their shareholders and stakeholders. Logistics services includes warehousing, freight, transportation, product return and repairs, inventory management, packaging, order entry/order processing. All these can be managed internally. But the challenges of coping with manufacturing and handling logistics which is not the core of the organization business model result to the outsourcing for logistics service providers, such as third-party logistics service providers. This paper aimed at investigating the moderating effect of innovation on logistics practices, particularly, warehousing, transport and packaging services, of 3PLs service provider in Malaysia manufacturing sector. Quantitative method of research was adopted, and questionnaire was distributed electronically. It was analysed using SPSS and the result indicated that innovation of green logistics moderates the relationship between inventory management and operational performance, packaging and service performance but does not moderate relationship between transportation and service performance.